My base assumption is that each season is roughly a calendar year. All timing below is based on that.
We're given almost no specific dates or times, so much of what's here is a guess.
I assume that aired canon happens chronologically unless we're told otherwise.

Break out of the frame | Updated April 12, 2006 | Get the frame back

Timeline

Ancient History | 0001-2001 | 2004 | 2005

For information about events in the home galaxy, see the SG1 Timeline.
Lines between entries are a basic 'time passes' indicator, for situations
where I don't know how much time has passed between events,
usually in different episodes.

Ancient History

5-10 million years ago | Several million years ago | ca. 8,000 BC | ca. 4700 BC | ca. 1400 BC

nb: 'ancient', not 'Ancient'

5-10 million years ago

The Ancients live on Earth, based in the city of Atlantis on the Antarctic continent. (Rising pt 1)

Several million years ago

The Ancients in the Milky Way are struck by a virulent plague that starts to wipe out the race. (SG1: Full Circle, Rising pt 1)

The Ancients leave Earth, flying off in the city of Atlantis, headed for the Pegasus galaxy. (Rising pt 1)

In the Pegasus galaxy, the Ancients begin seeding new (human) life on at least a thousand worlds. (Rising pt 1)

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ca. 8,000 BC

(10,000 years ago)

The Ancients wake the Wraith and become embroiled in a war they're not prepared for. (Rising pt 1)

The war with the Wraith lasts roughly one hundred years. (The Siege part 2)

The Ancients install a weapons platform in a Lagrangian Point orbit around another planet in the Atlantica solar system, as part of their last line of defense against the Wraith. (The Defiant One)

The satellite takes out a Wraith supply ship, sending it crashing to the planet below. (The Defiant One)

An Ancient steps through the stargate on Dagan bearing a ZPM and entrusts it to a sect of Suderian priests (the Brotherhood of Fifteen, or Quindozum), charging them to keep it safe from the Wraith at all costs. (The Brotherhood)

Athar (aka Chaya Sar) ascends, but can't cut her ties with the humans she's been living among on Proculus. She uses her ascended powers to defend them from the Wraith. In punishment, the Others exile her on Proculus, where she can defend the Proculans but no one else. (Sanctuary)

The Atlantians send a delegation to try to negotiate a truce with the Wraith. They're protected by their most powerful warships, to no avail -- there are too many Wraith. (Before I Sleep)

After the big battle from the failed negotiations, the Atlantians give up, and begin readying to evacuate back to Earth. (Before I Sleep)

Weir, Sheppard, and Zelenka arrive in a 'gateship' (puddlejumper) over Atlantis after accidentally traveling back in time some 10,000 years. They're caught in a Wraith attack and shot down. Sheppard and Zelenka both die, but Weir is brought back to Atlantis and healed (by Janus). (Before I Sleep)

The Atlantian Council refuses to send Weir back to her own time, inviting her instead to go back with them to Earth. Janus argues, to no avail, so comes up with another plan -- putting Weir in stasis to revive every 3.3 thousand years to rotate the city's three ZPMs, so the city can draw power in sequence rather than in parallel, squeezing out every last drop of power. He reconfigures the city's power systems to do just that, and sets a failsafe mechanism to break the city free of the ocean floor in the event Weir dies in stasis and power drops to critical levels. He also blocks all incoming addresses other than Earth, to keep her safe. (Before I Sleep)

A transport ship carrying some 300 people is destroyed by Wraith while inbound to Atlantis. Either this is the final transport, or the losses are getting too close to the city -- Councilor Moros declares that the evacuation must begin immediately. (Before I Sleep)

Janus and the other Ancients evacuate the city for Earth, while Weir secretly stays behind to carry out the plan, shutting down the city and going into stasis. (Before I Sleep)

The Brotherhood of Fifteen (the Quindozum) are culled in a Wraith attack, leaving the ZPM, or potentia, hidden safely away for millennia. (The Brotherhood)

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ca. 4700 BC

Original-timeline Elizabeth Weir wakes up from stasis and rotates Atlantis's ZPMs to put a fresh one in position as main power source, then goes back into stasis. (Before I Sleep)

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ca 1400 BC

Original-timeline Elizabeth Weir wakes up from stasis and rotates Atlantis's ZPMs to put a fresh one in position as main power source, then goes back into stasis. (Before I Sleep)

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0001-2003

ca. 1500 | ca. 1850 | ca. 1998

ca. 1500

Roughly when the inhabitants of M76-677 put up an electromagnetic shield around a small portion of their world, and instituted ritual sacrifice of everyone on the eve of their 25th birthday as a population-control measure. (Childhood's End)

Roughly when the most recent visitors before Sheppard's team visited the kids' world via stargate. (Childhood's End)

Roughly when the Wraith last visited the kids' world. (Childhood's End)

nb: it's not clear if both of those events were the same thing. (Childhood's End)

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ca. 1850

The last great Wraith holocaust/culling happened. (Rising pt 1, Poisoning the Well)

Teyla said this happened 'five generations ago' -- a generation is usually 20-25 years, but may be closer to 30 for Athosians. (Rising pt 1)

Druhin specifically said that the Hoffan scientists were close to a viable prototype on their drug 150 years ago, but died before they could complete it -- likely from a major culling. (Poisoning the Well)

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ca. 1998

Ronon Dex is culled from his homeworld. When the Wraith can't feed on him, they insert a tracking device into his back and set him 'free' as a runner, to be hunted down wherever he goes until they kill him. (Runner)

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2004

early 2004 |  mid-2004  | late 2004

early 2004

Original timeline

The expedition from Earth steps through the stargate, triggering Atlantis's basic systems (lights, doors, air circulation), which causes too great a drain on the power sources, and the city's shields begin catasrophically failing. Almost the entire expedition winds up drowning as the city floods -- the only exceptions are Sheppard, Weir, and Zelenka, who were in a 'gateship' (puddlejumper) equipped with a time-travel device. They escaped by inadvertantly traveling back in time 10,000 years. (Before I Sleep)

Current timeline

An expedition from Earth arrives on Atlantis. (Rising)

The city's shields begin to fail, and the expedition sends a team offworld to search for a world to evacuate to. (Rising)

The offworld team discovers the Athosians, but gets caught in a Wraith raid. The remaining Athosians return to Atlantis with the remaining team members, as refugees. (Rising)

As the city's shields go critical, a failsafe mechanism kicks in, and the city rises to the surface, safe from being flooded/crushed beneath the water, but with no protective shields anymore. A rescue team heads off to find the Wraith captives. (Rising)

The expedition suffers its first casualty when Colonel Sumner dies while in Wraith hands (by way of a mercy killing by Sheppard). (Rising)

Sheppard inadvertantly wakes the hibernatitng Wraith when he kills their caretaker, loosing them on the galaxy. (Rising)

This is roughly 50 years before the Wraith would have woken up on their own. (Poisoning the Well)

The captives are freed, and the Athosians and Terrans celebrate their survival on Atlantis. (Rising)

A couple of days later

McKay is successfully given the ATA gene therapy and becomes able to use Ancient technology. (Hide and Seek)

Jinto accidentally releases a shadow entity that feeds on energy, which begins to drain the city's power. (Hide and Seek)

McKay saves the city by putting on his personal shield and wading into the now-massive energy field to grab a case holding an active naquadah generator, which the entity is feeding on, and flinging it through an open wormhole to a barren world. The entity follows. (Hide and Seek)

On a mission to the Wraith world where the captives had been held, the team runs into some Wraith and has to make a run back for the puddlejumper. Sheppard stumbles into a web and is stung by a deadly bug -- deadly enough that when a Wraith spots him, he takes one look and wanders off again, clearly believing that Sheppard is done for. (Thirty-Eight Minutes)

On the way back to Atlantis, the damaged puddlejumper gets stuck halfway through an active stargate, leaving the team and the scientists back on Atlantis just under 38 minutes to figure out a way to fix the problem from inside the jumper. (Thirty-Eight Minutes)

To save Sheppard's life, Ford winds up using a defibrillator to kill him temporarily, causing the bug to let go. Teyla carries Sheppard into the wormhole in the hope that if the jumper is repaired in time, they'll all rematerialize on the Atlantis side, with enough time to save him. (Thirty-Eight Minutes)

The repair work succeeds, and Sheppard is revived. (Thirty-Eight Minutes)

Three months after arrival on Atlantis

By the time the primary team has run into Wraith five times in nine missions, Weir decides there must be a spy in their midst, likely an Athosian. She and Bates begin a security crackdown, complete with fairly aggressive interviews of all the Athosians. (Suspicion)

Weir suspends all gate travel until further notice. (Suspicion)

Zelanka and McKay accidentally manage to open the roof of the jumper bay, allowing exploration of the planet by air. Sheppard and Ford make the first trip and promtply discover a landmass, roughly 15 million square miles, about 25 minutes from the city by jumper. (Suspicion)

The Athosians, fed up with being treated like prisoners under house arrest, move to the mainland to explore it and set up a camp. (Suspicion)

The Wraith attack another offworld mission, made up of Sheppard's and Stackhouse's teams, convincing Bates that Teyla is the spy. Closer examination shows that she's been inadverantly carrying around a transmitter that the Wraith have been homing in on. (Suspicion)

A mission is put together to trap a Wraith using the transmitter as bait. It succeeds. (Suspicion)

Three months, one week after arrival on Atlantis

The Athosians on the mainland are already busily planting crops. (Suspicion)

Sheppard's team crash-lands on a planet when an electromagnetic disturbance takes out all their controls. (Childhood's End)

McKay removes the ZPM from an EM-field-generating device on M76-677 and brings it back to Atlantis to study. A Wraith bracelet on a skeleton, dormant for years, activates when the EM field is removed, sending a signal to the Wraith. McKay returns the ZPM and gets it working just in time to kill a Wraith probe that was scanning for information, prior to a Wraith attack. (Childhood's End)

The sacrifices on M76-677 are stopped after all the village elders hear the truth behind the reason for them. (Childhood's End)

Three-and-a-half to four months after arrival on Atlantis

Sheppard's team travels to Hoff, spending two days getting to know the people and being toured around before being told that the Hoffans are working on a defensive weapon against the Wratith -- a drug that will make them immune to the chemical the Wraith use to trigger the draining of human lifeforce. (Poisoning the Well)

Sheppard goes to talk to the captured Wraith, whom he names ' Steve' , telling him 'we've been having these conversations for a couple of weeks now...' (Poisoning the Well)

The team brings Steve back to Hoff to subject him to a test of the drug (without his knowledge or consent -- he believes he's being fed in exchange for information). He gives them some information and tries to feed, but the drug works -- better than anyone expected. It kills Steve when it mutates into a toxin in his bloodstream. (Poisoning the Well)

The Hoffans push forward into widespread innoculations. Soon after, 50% of the people innoculated die of acute respiratory failure, but the Hoffans believe that's an acceptable mortality rate given the ultimate advantage over the Wraith that the drug confers. They continue with innoculations. (Poisoning the Well)

Sheppard and his team, along with Beckett and the remaining Atlantis personnel, leave the planet, with no intentions of coming back. Sheppard flatly refuses to help Druhin distribute the drug among other human worlds, telling him that he expects the Hoffans to all be 'gone' (dead) if and when the team ever returns. (Poisoning the Well)

Coffee is starting to run low on Atlantis, and other supplies are reaching the point of near rationing. (Underground)

Teyla introduces her team to the Genii. After a rough start, they ally with the Genii to help them implement their plan to use an A-bomb against hibernating Wraith. (Underground)

During the recon mission to see if the plan is even possible, Tyrus of the Genii kills a human captive of the Wraith to keep Teyla from freeing him (which would give away their presence -- although killing him does the same thing), and is promptly shot by a Wraith. (Underground)

The alliance turns to declared enmity after the recon mission, when Cowen of the Genii springs a trap on the Atlantians, who counter with decloaked jumpers in position to fire on the Genii. By the end, the Atlantians have taken the intell recovered from the Wraith and left, with angry, mistrustful Genii left behind to stew. (Underground)

Sheppard's team discovers a world giving off widespread energy readings, but with no evidence of civilization -- just lots of fog/mist, and a few standing stones near the stargate. When McKay notices energy spikes as the stargate is dialed up, he concludes that the gate could draw on the energy being generated in the atmosphere/fog, possibly enough to make a connection back to Earth. (Home)

The team and Weir return to the planet hoping to contact Earth, but the energy beings who make up the mist covering the world knock them out and put each in a fabricated reality, to keep them from activating the gate and killing millions of the energy beings with the drain from the connection. (Home)

Everyone figures out that the reality they're experiencing is false (Sheppard guesses first), and the energy beings admit what they've done, and why. The Atlantians promise to gate straight back to Atlantis and never return. The energy beings let them go. (Home)

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mid-2004

A megastorm is threatening both the mainland settlement and Atlantis, and all but a handful in each place evacuates to Manara, hoping to wait out the storm for a day or two and then be able to return. (The Storm)

Smeadon of the Manarians contacts the Genii to tell them about Atlantis's window of vulnerability. (The Storm)

The Genii send a strikeforce to Atlantis, led by Commander Acasustus Kolya. They gain access disguised as wounded Athosians, using a stolen Athosian IDC. Kolya kills the two guards who let them through. (The Storm)

Weir and McKay are captured by the Genii, and forced to give up information that Kolya wanted about the location of supplies and the plan to save the city. Kolya changes his focus to taking the city instead of raiding it. (The Storm)

Sheppard starts a running battle with the Genii soldiers in the city, winning every encounter. He and Kolya begin taking it personally, as he kills more of Kolya's men and Kolya threatens Weir and McKay. (The Storm, The Eye)

Sora of the Genii finds Teyla and challenges her to hand-to-hand combat (with knives) in order to avenge her father's death. (The Eye)

McKay finishes the work needed to turn the entire city into a superconductor, but the experiment appears to fail, with not enough power getting to the shields to activate them. Kolya orders his men to retreat back through the stargate, taking McKay and Weir along. Before they can get away, Ford and Sheppard open fire, saving McKay, then Sheppard shoots Kolya in the shoulder, forcing him to release his grip on Weir. Kolya falls back through the stargate -- bitter and angry. (The Eye)

Teyla beats Sora but lets her live. (The Eye)

McKay gets the shield working bare seconds before a massive wave swamps the city. (The Eye)

All the evacuees return home. Sora is in custody. The city is flooded in parts, but salvageable. (The Eye)

The Genii send offworld agents to spy on the activities of any Atlantian teams they can find. (The Brotherhood)

Dr. Brendan Gall discovers an Ancient satellite in a Lagrangian Point orbit around another planet in the solar system, and a team consisting of him, Dr. Abrams, Sheppard, and McKay go to investigate. After a 15-hour puddlejumper trip, they discover a crashed Wraith supply ship. (The Defiant One)

The lone Wraith still hibernating on the ship wakes up and attacks Abrams and Gall, killing Abrams and paralyzing Gall. He takes over the jumper, then he and Sheppard fight it out. The Wraith is hurt, but each encounter leaves him alive and still in charge of the jumper. (The Defiant One)

Gall shoots himself to free McKay to leave him and go help Sheppard. (The Defiant One)

Sheppard and McKay run out of ammo trying to kill the Wraith, and are in a bad spot until Ford checks in from space, where his puddlejumper is close enough to fire. Sheppard slaps a powerbar onto the Wraith to attrack the local tiny energy beings, and Markham, aboard the jumper, shoots at the Wraith, now a big enough target to differentiate. The Wraith is finally killed. (The Defiant One)

McKay takes a team of scientists and a few military personnel (as guards) on a survey of at least part of the outlying regions of the city, checking for damage after the storm. As they're wrapping up, two of them suffer horrific hallucinations and drop dead, causing McKay to call for a containment team and Zelenka to suggest a level-four quarantine of the group. Weir institutes a self-regulating quarantine for the rest of the city to be safe. (Hot Zone)

Peterson sneaks away from the quarantined group when he begins seeing things, and begins making his way back to the main city. McKay begins suffering small hallucinations, easy to ignore. (Hot Zone)

Sheppard argues with Weir about breaking quarantine, then orders Bates to open the door locking him in. Weir countermands the order. Sheppard orders Bates again, and Bates reaches past Weir to open the door for him. This requires powering up the entire section, including the transporters, which had been shut down for the quarantine. (Hot Zone)

McKay's small hallucinations get bigger, and Hayes admits to suffering them as well. (Hot Zone)

Sheppard and Teyla find Peterson in a hall, but he makes a break for a transporter nearby. Sheppard shoots him, but he manages to activate the transporter and makes it to the mess hall, where around 25 people are quarantined. He dies moments after he arrives. (Hot Zone)

Hayes, infected at the same time as McKay, suffers a final hallucination and then dies of a brain aneurysm above his visual cortex. (Hot Zone)

The city institutes a lockdown as soon as it senses the viral infection in the mess hall. (Hot Zone)

McKay fails to die, and the general consensus is that it's because he's got the Ancient gene. (Hot Zone)

McKay and Beckett determine that the virus must actually be a nano-virus, specifically designed to first terrorize then kill, all within exactly six hours of infection. And it's desgned specifically to kill humans, since the Ancient gene stops the final stages from happening. (Hot Zone)

Once he knows it's a machine, McKay figures out how to fix it -- with an EM pulse. He has Sheppard generate one from an EMP  machine in McKay's lab, but it's not powerful enough to do the job. With less than half an hour to go before the next victims (Zelenka and Ford) die, McKay and Sheppard talk Weir into okaying a nuclear blast. Sheppard carries a naquadah generator 20 miles up into the atmosphere in a jumper, and releases it to overload and explode, bathing the city in a massive EM pulse but keeping it safe from radiological harm. It works -- the nanovirus is completely destroyed. (Hot Zone)

Sheppard's team discovers a world -- Proculus -- with a powerful weapon against the Wraith, which they assume is ZPM-driven. When they go to investigate, they discover that the Proculans have never even heard of the Wraith, and believe themselves to be protected by their goddess, Athar. When the team approaches the high priestess, Chaya Sar, to request access to the ZPM, or at least permission to allow refugees to claim sanctuary on this protected world, she goes to ask Athar and returns with the news that she can allow neither. Sheppard presses the matter and she agrees to return to Atlantis to learn more. (Sanctuary)

Sheppard and Chaya move past flirting. (Sanctuary)

McKay, highly suspicious of Chaya, surreptitiously puts monitors on her, and discovers that she's actually an ascended Ancient. Chaya is pissy at having been found out, and when she realizes that her world is being attacked, races back through the stargate to defend it. Later, she tells Sheppard that she's exiled there, for the crime of defending the Proculans after she ascended originally -- but that part of her punishment is that she can only help the Proculans, no one else. (Sanctuary)

The Elizabeth Weir from the original timeline is discovered in a stasis chamber and revived, and tells the story of the original expedition and how she traveled back in time. She dies almost as soon as she's been able to tell them everything -- including that the note she brought with her held the gate addresses to five  outposts, each with a ZPM. (Before I Sleep)

Elizabeth scatters her 'own' ashes over Atlantis. (Before I Sleep)

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late 2004

Roughly a month before the Wraith arrive over Atlantis, the expedition discovers and brings online a biometric sensor in the control room, narrowing its focus to the gateroom to conserve power. The sensor scans and reports any biometric irregularities. (The Siege part 1)

Sheppard's team goes to Dagan and begins working with the Daganians to search for a ZPM that they believe is hidden on the planet. Genii spies see them there and report back that their search for an Ancient power source appears to be going well, and Kolya travels to Dagan personally. (The Brotherhood)

Zelenka discovers Atlantis's long-range sensors. (The Brotherhood)

Kolya captures Sheppard's team on Dagan and begins his own search for the ZPM, planning to take it for himself (and the Genii). (The Brotherhood)

Markham and Smith are killed in a puddlejumper while trying to protect Atlantis from a Wraith dart. (The Brotherhood)

A Wraith dart scans at least part of the city and then self-destructs before the jumpers following it can destroy it. (The Brotherhood)

The ZPM is found, and while Kolya and his people are distracted by it, Sheppard's team jumps them, injuring most of them and winning the ZPM back. They leave Kolya alive and head back to the village, but on the way are ambushed by Daganians who have recreated the Brotherhood of the Fifteen (Quindozum) and believe that their duty is to keep the ZPM hidden. The Daganians take the ZPM to hide on another world and send the Atlantians packing back home. (The Brotherhood)

The Atlantians discover that there are three Wraith hive ships headed directly for them -- at their current speed, they'll be over Atlantis in two weeks. (The Brotherhood)

With three Wraith hive ships just two weeks away from Atlantis, McKay refines a data-compression process to allow the expedition to send as much information as possible back to Earth in a single data burst through the stargate. The burst includes all official information (mission reports, tactical situation, etc.) and personal messages from anyone who wanted to send one. (Letters From Pegasus)

Roughly one week after it's discovered that the Wraith are on the way -- meaning they're now about one week away -- the Atlantis expedition has located a possible alpha site for evacuation. Bates's team completes the ground and aerial surveys, determining that it's an appropriate site, and Sheppard goes to give it a final check. He approves it, but as they're leaving, the Wraith arrive and 'tag' the planet, making it unusable. The expedition must begin searching for more sites. (The Gift)

Teyla is having severe Wraith-related nightmares, disturbing her sleep badly enough that Sheppard can beat her when they're sparring with sticks and she becomes snappish with everyone. Despite some strong initial misgivings, she visits Heightmeyer to help sort it out, and decides it's related to her ability to sense Wraith. From there she visits Beckett to see if that ability is biological -- when he can't tell her, she goes to the mainland to talk to Charin, who tells her of a planet where people taken by Wraith were sometimes returned, and how one of those people is part of Teyla's lineage. (The Gift)

At Teyla's request, Sheppard's team goes to the world where humans were taken and returned, and they discover an old, abandoned Wraith laboratory. Rodney manages to salvage a data recorder. (The Gift)

Despite finding out some of the background to her gift, Teyla's nightmares get worse. (The Gift)

Weir manages to translate part of the data recorder and gets Beckett to run some genetic tests to confirm what she found, then they break the news to Teyla: she has some Wraith DNA in her genetic makeup, as a result of experiments performed on one of her ancestors. (The Gift)

After some disbelief, Teyla agrees to be hypnotized to try to tap into the Wraith telepathic network. It works, but it works two ways -- while she's looking through Wraith eyes, a Wraith can get inside her head and look through hers. On her third try, a Wraith settles in so solidly that giving her a shock no longer snaps her out of it -- Bates has to hit her twice with a Wraith stunner to knock the Wraith in her out. (The Gift)

Teyla wakes up and tells Weir and the others that the Wraith aren't coming to Atlantis just to feed -- they're coming to gain access to Earth, and the rich new feeding ground it will be. (The Gift)

With 49 hours to go before the Wraith's expected arrival, McKay (and Zelenka) put for the idea of using a naquadah generator to power the Ancient weapons platform in Atlantica's system -- the Wraith think it's dead, so powering it up will give them the element of surprise in the invasion. (The Siege part 1)

Teyla is released back to active duty, from her medical confinement after her mental interactions with the Wraith. (The Siege part 1)

Sheppard, Teyla, and Ford check out M1M-316 as a possible alpha site but are attacked by what looks like a T. Rex. Afterwards, not knowing it was an animal that attacked the team, Bates accuses Teyla of inadvertantly giving their position away to the Wraith because of her connection to them. Teyla loses her temper, follows him, and slugs him. (The Siege part 1)

Six days before Weir travels to the Genii homeworld, the Wraith arrive on that world and cull hundreds of people, but thousands remain safe underground. (The Siege part 2)

About  15  hours  after  leaving  Atlantis by puddlejumper,  a small team (McKay, Grodin, Miller) arrives at the weapons platform and begins powering it up. (The Siege part 1)

Zelenka develops a computer virus capable of wiping out the Ancient database, to be used along with the self-destruct in case the Wraith seem likely to gain the city. (The Siege part 1)

Bates is viciously attacked, resulting in five broken ribs, a fractured collarbone, and a severe concussion, and placed in a medical coma while the medical staff deals with his subdural hematoma. (The Siege part 1)

Five hours after arriving at the weapons platform (with 29 hours to go before the Wraith arrive), McKay and Grodin figure out that the weapon isn't getting power even though the buffer that feeds the weapon is nearly fully charged. They decide to reroute the power, then realize the circuits are outside, and that someone will have to go EVA. With Miller, they play rock-paper-scissors, resulting in a three-way draw, then Miller splits a pencil into three and they draw 'straws'. McKay loses, and suits up. Miller brings him in the puddlejumper to the area he needs to do the work on, while Grodin remains on the satellite. Rerouting the power works but disables the docking and airlock mechanism, trapping Grodin on the satellite. (The Siege part 1)

Beckett runs two tests on DNA found in Bates's clothing and confirms conclusively that it was a Wraith who attacked him, and is now loose in the city. Zelenka recalibrates the city's biometric sensor to cover the entire city, and locates the Wraith immediately. Sheppard takes a team to find him, while Ford and Teyla take another team to come at him from another direction. The Wraith stuns Sheppard's team, but is stunned in turn by Ford and Teyla's team and is taken prisoner. (The Siege part 1)

The Wraith fleet makes it to Atlantis's system, and the first hive ship is destroyed by the satellite as planned. The rerouted circuits overload, making it impossible for the weapon to fire again, and before Grodin can even begin to try fixing it, the remaining Wraith ships destroy the satellite with Grodin aboard it. (The Siege part 1)

Weir calls for evacuation of the city. (The Siege part 1)

Sheppard kills the captured Wraith, 'Bob', in the holding cell. (The Siege part 1)

Roughly 15 hours after the satellite is destroyed, the evacuation is nearly complete, with only one group and the people manning the control room still to leave. Weir and Sheppard set the auto-destruct for ten hours, and Weir orders the database-destroying virus to be loaded into the city's mainframe. (The Siege part 2)

Before they can dial out to the alpha site, Stargate Command dials in, and relief troops headed by Colonel Everett come through the gate, relatively up to speed on the situation thanks to the message the expedition had sent back. He takes command of Atlantis -- both Weir's job and Sheppard's -- and rescinds the evacuation notice, recalling all military personnel and any civilians who want to help. (The Siege part 2)

nb: This aligns perfectly with the end of SG1 season 8, when the SGC got hold of a working ZPM. The events of Siege parts 1 & 2 must happen immediately after Moebius part 2.

The relief forces bring six naquadah-enhanced nukes, several rail guns, and a Mark II naquadah generator to power the chair platform. (The Siege part 2)

Four new pilots are given the ATA gene therapy, which appears to take effect on all four. Sheppard trains them in how to fly a puddlejumper, and they all head out to deploy naquadah-enhanced nukes acting as space mines. (The Siege part 2)

Beckett powers up the chair once it's hooked up to the Mark II naquadah generator. Once it's powered up, it becomes clear that there are only a few dozen drones ('energy squids') left available to the city. (The Siege part 2)

The Wraith harvest asteroids and accelerate them in Atlantis's general direction. They aim for the mines that have just been deployed, and take out all six, creating enough residual radiation to shield the hive ships's approach from the city's sensors. (The Siege part 2)

The Wraith launch an attack by darts against the city. Atlantis's sensors don't spot them until they're almost on top of the city, leaving the expedition little time to react. During the attack, 20-30 Wraith aim their darts straight at the city in kamikaze runs and beam out into the city before their ships crash. (The Siege part 2)

McKay gets the chair powered up again, and Sheppard launches several drones against the attacking darts. Between that the the rail guns, the city holds out for the moment. (The Siege part 2)

On Sheppard's suggestion, McKay and Zelenka begin working on a way to remote-control a puddlejumper, to use them as weapons directly against hive ships. Also on Sheppard's suggestion, Atlantis contacts the Genii, in hopes of gaining access to their nuclear weapon to use against the Wraith. (The Siege part 2)

Teams, including Athosians, spread out throughout the city to track down the Wraith. (The Siege part 2)

Weir is granted access by the Prenum of the Genii, and steps through the stargate to negotiate. She's taken blindfolded to an underground bunker, where Prenum informs her that she's being held so that he can trade her back to Atlantis for C-4 (to incorporate into their nukes). She points out that she was offering the C-4 regardless, and that rather than wasting their tests on nothing, they now have the chance to test their weapons against hive ships, with no risk to themselves. Prenum goes for it, and returns her to Atlantis with the prototype weapons. (The Siege part 2)

McKay and Zelenka manage to hook the chair platform up to the puddlejumpers remotely, so that someone sitting in the chair can operate a puddlejumper -- specifically to use them against the hive ships approaching Atlantis. (The Siege part 2)

McKay determines that the Genii prototype weapons are incomplete, and that he'll need about a day to finish them. He and Zelenka get to work. (The Siege part 2)

The prototypes are completed and loaded on jumpers just as a new wave of Wraith darts attacks the city, but the Mark II is depleted -- they can't be operated from the chair. Sheppard goes to the jumper bay to fly one manually against the hive ships. (The Siege part 2)

Everett is caught by a Wraith, who begins feeding on him. (The Siege part 2)

Ford and his team are trapped by two Wraith groups that beamed in in front of them and behind them. (The Siege part 2)

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2005

late  2004/early  2005  |  early 2005 | 

late 2004 / early 2005

The Daedalus, a BC-303 from Earth commanded by Colonel Steven Caldwell, rescues Sheppard just before the bomb he sent toward one of the hive ships explodes, destroying the hive ship and Sheppard's puddlejumper. Sheppard contacts Atlantis moments later (to their surprise -- they thought he died in the hive ship's explosion), and Caldwell's people beam down a crated ZPM for McKay to use to power the city's shields. The Daedalus takes on the remaining hive ship while Atlantis continues dealing with the Wraith inside the city. (The Siege part 3)

With Hermiod's (cranky) assistance, the Daedalus beams a warhead aboard the last remaining hive ship and destroys it. The cruisers accompanying the hive ship flee into hyperspace, leaving a lot of darts behind, which break off from the Daedalus to attack the city at a ballistic approach velocity -- set to impact at more than 10,000 kilometers per hour. McKay gets the ZPM installed and Zelenka gets the shield raised just seconds before impact, saving the city. (The Siege part 3)

The last Wraith in the city dies trying to detonate a grenade. (The Siege part 3)

Prelimary estimates put the human casualties at 40, maybe more. (The Siege part 3)

Ford is rescued from the ocean, where he's been lying face-down in freezing water for more than an hour, kept alive by an abundance of Wraith feeding enzyme that flooded his system when the Wraith attacking him died suddenly. (The Siege part 3)

12 more hive ships are spotted heading for Atlantis, set to arrive in about 36 hours. (The Siege part 3)

With just over a day to go before the new hive ships arrive, Sheppard proposes that they take the fight to the Wraith, rather than waiting to be attacked. Weir and Caldwell agree. The plan works as far as it goes -- the Daedalus takes out two of the new hive ships before they know what's happening. The Wraith institute countermeasures that prevent the Daedalus from beaming anything else aboard their ships, changing the tenor of the battle. With now-protected hive ships closing in, and its own shields dangerously weakened, the Daedalus is forced to run for home, and lands on Atlantis for the first time -- Caldwell wants to repair the shields beneath the safety of Atlantis's stronger shield before risking exposure again. (The Siege part 3)

As the hive ships begin their attack on Atlantis, Ford attacks a guard and threatens a patient in the infirmary to force Beckett to hand over all the harvested enzyme, then flees into the city. (The Siege part 3)

With no way to defeat the Wraith -- even if they manage to win this battle, more hive ships will come, then more, and the ZPM isn't sufficient to shield the city for more than a few days under constant bombardment -- Sheppard proposes that they fake a self-destruct by beaming a nuke directly above the shield and detonating it, then cloaking the city. McKay and Zelenka agree that it's possible, and Weir approves the plan. All non-essential personnel are told to evacuate to the Daedalus in case the plan fails. (The Siege part 3)

Once McKay and Zelenka have the cloak ready to go, and everyone possible has been evacuated to the Daedalus -- with Ford still in the city and Sheppard searching for him -- Teyla makes mental contact with the Wraith to convince them that the expedition plans to destroy the city rather than let it fall into Wraith hands. The Wraith believe it and stop their bombardment, not wanting to contribute to the destruction of their only route to Earth. The nuke and cloak work as planned -- the Wraith scan for the city after the explosion but don't see it. (The Siege part 3)

Ford, believing that Sheppard and the others want to 'change [him] back', heads for the jumper bay and knocks out Zelenka, then grabs a jumper and heads through the stargate for parts unknown, disobeying a direct order from Sheppard to stand down. (The Siege part 3)

After the siege, Weir, Sheppard, McKay, Beckett, and others return to the SGC through the stargate to be debriefed and take care of other administrative details. The Daedalus makes the trip back through space as usual. (The Intruder)

The international committee approves a significant increase in personnel and resources  for the Atlantis mission. (The Intruder)

Landry tells Weir that Sheppard poses a problem -- his independent nature may mean he could choose do disobey the new military commander. Weir is taken aback, and points out that Sheppard is the military commander. Landry agrees that Sheppard acted correctly in assuming command, but only until a proper replacement for Sumner could be brought in, and suggests that Caldwell -- although not confirmed in the position yet -- is that replacement. When Caldwell points out that a mission as important as Atlantis shouldn't be trusted to a mere major (especially with Sheppard's background), Weir tells him that Sheppard's background doesn't matter to her, and informs Caldwell and Landry both that if Sheppard's rank isn't high enough for them, they'll just have to promote him. (The Intruder)

At Weir's strong insistence (almost threatening General Landry into it), Sheppard is promoted to lieutenant colonel and officially given military command of Atlantis.  Caldwell wasn't thrilled -- he'd expected the command for himself. (The Intruder)

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early 2005

Nearly a month after Sheppard is promoted to lieutenant colonel, the Daedalus has nearly completed its 18-day trip back to Atlantis with the Atlantis personnel aboard. (The Intruder)

Less than two days out from Atlantis, Doctor Monroe dies aboard the Daedalus as a result of an apparent power surge that electrocutes him. Caldwell at first refuses to drop the ship out of hyperspace, since it would leave them exposed to detection, but as soon as McKay discovers that it might not have been an accident, Caldwell gives the order and the Daedalus drops out into normal space. (The Intruder)

During the investigation into what caused the power surge that killed Monroe, Lindstrom discovers something that may provide a clue. Immediately, a coolant leak is triggered in the room where he and McKay are working, forcing Lindstrom to shelter in an airlock to escape the toxins. Moments later, the airlock opens -- with the controls not responding to Lindstrom's attempts to override them -- and Lindstrom is spaced. He dies within seconds. (The Intruder)

Caldwell confines all civilians (barring Weir, McKay, and probably Beckett) to quarters in an attempt to curb possible future sabotage, saying he can't  blindly trust any of them since he had no say in their selection. (The Intruder)

Hermiod discovers the source of the sabotage: a computer virus so advanced that it's effectively an AI, capable of adapting and defending itself, which McKay figures out is Wraith in origin. It has spread through the navigation system and into the communications and propulsion systems, likely embedding itself so deeply that it can't be isolated without crippling the ship. McKay deduces that the intent behind the virus is to take over the ship's navigation completely, and fly it straight to the Wraith, giving them not only access to the intergalactic hyperdrive but also to navigational info that would lead them straight to Earth. (The Intruder)

With the ship at a virtual standstill in normal space and without enough navigational control yet to fly it to the Wraith, the virus changes tactics and begins broadcasting a distress signal, to draw the Wraith to the ship. (The Intruder)

Sheppard takes an F-302 out to shoot out the transmitter array. He succeeds, but the virus has infected his ship and locks the controls to send him speeding away from the Daedalus. McKay and Hermiod manage to beam him back aboard by locking on to his radio signal. (The Intruder)

McKay does a complete shutdown and reboot of the system, reloading everything from backups to clear the virus out. It appears to work until they engage the sublight engines, at which point the virus -- which has been hiding out in the F-302s -- reappears and takes control of the Daedalus, sending it on a course for the coronasphere of the nearest star, planning to kill all the people aboard while salvaging the ship itself. Sheppard and McKay go to physically remove all the memory from the F-302s, nearly getting killed by the virus in the process. The next reboot fails as well, and Sheppard realizes they missed one F-302: the one he'd been flying and had been rescued from. He and McKay fly out in the 302 they've been sheltering in and destroy the virus-controlled one, allowing the Daedalus to reboot cleanly and return safely to Atlantis. (The Intruder)

On P3M-736, Ford saves Ronon Dex's life more or less inadvertantly -- he kills the Wraith who was chasing Ronon, to gain access to the Wraith's enzyme sack. (Runner)

Roughly a week after the Daedalus returns from Earth with new personnel and supplies, Major Lorne's team finds a dead Wraith offworld. Beckett discovers that its enzyme sack has been removed, leading to speculation that it was Ford who killed it. Sheppard assembles a team to go hunt for him. (Runner)

During the hunt, Sheppard and Teyla are captured by Specialist Ronon Dex, who has been on the run from Wraith for years. Lorne takes command of the search, with additional personnel. When he and McKay run into Ford, Lorne is knocked out with a Wraith stunner and McKay is dragged off by a completely nutso Ford on a random journey through the forest, ostensibly to rescue Sheppard and Teyla, while Ford veers between (sincere) cheery camaraderie and  (equally  sincere) psycho threats. (Runner)

Sheppard makes a deal with Ronon: they'll get the tracking device out of his back and not interfere with his leaving the planet if he lets them go. He agrees to that, and to help them capture Ford, if they can really get the device out. Sheppard runs back for the jumper to go to Atlantis to fetch Beckett, who is less than thrilled to be asked to do surgery outside on another planet on someone holding Teyla hostage. He does it, though, and successfully removes the tracker. (Runner)

McKay shoots Ford in the arm and escapes, only to get caught up in one of Ronon's snares. Ford finds him but is tackled by Ronon, who is trying to live up to his side of the bargain with Sheppard. They fight with fists and knives, but are interrupted by Sheppard, holding a P-90. Ford runs. Sheppard follows and winds up shooting him in the leg to try to get him to surrender. For, shouting 'you'll see!', runs straight into the path of a Wraith culling beam, apparently on purpose. (Runner)

Ronon returns to Atlantis with the others, where he's held in light confinement (guards, but comfortable surroundings). The expedition sends a MALP through to the coordinates he gives them for his homeworld, only to find a ruined, smoking city and no sign of life. (Runner)

While searching a culled world for survivors, McKay and Lt. Cadman are culled by a dart that came through the stargate. The combined efforts of the expanded team that is on the planet (Sheppard's, Lorne's, and a Marine team) bring the dart down, trapping McKay and Cadman inside. Zelenka is brought in and discovers that the mechanism to rematerialize captives is damaged, with only enough remaning power to bring one lifesign out. Sheppard points to one and Zelenka activates the maching, rematerializing McKay, who passed out almost instantly. When he wakes up, he realizes that Cadman's consciousness is inside his mind. (Duet)

With Cadman in his head, McKay starts making mistakes in his calculations, causing a slight explosion during attempted repairs on the dart. Zelenka calls him on it and kicks him out, telling McKay to trust him to handle the problem. (Duet)

Ronon Dex begins what Sheppard considers training and Ronon considers testing -- sparring with several soldiers and being checked out on various Earth weapons (P-90, handgun) (Duet)

Cadman takes over McKay's body while he sleeps, tricking Beckett into joining McKay the next day on his first date with Katie Brown and then going for a workout/run. (Duet)

The next day the date goes ahead, with the addition of Beckett and Cadman. (Duet)

Sheppard offers Ronon a spot on his team - Ronon agrees to think about it. (Duet)

After a failed experiment trying to 'cull' and rematerialize two mice, McKay goes back to Heightmeyer, convinced he'll have Cadman in his head forever. They get into an argument that eventually pushes McKay's body into a seizure, knocking him out and putting him back in the infirmary. (Duet)

After they wake up, Beckett explains that one of them will have to completely let go all control of the body. Cadman says that whichever one does will just fade away -- it's already getting harder for her to be there, and Rodney's feeling the effect as well -- and volunteers herself to be the one to let go. (Duet)

McKay figures out that they can use a control crystal from the gate to stabilize the dematerialize/rematerialize cycle, and leaves the infirmary to get it done before the next seizure strikes. (Duet)

The process works, and McKay and Cadman are successfully rematerialized into their own, separate bodies. (Duet)

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