Episode 1 : Rising, Pts. 1 & 2
The Stargate SG-1 team discovers what they believe to be the remnants of the lost city of the Ancients ? the originators of the Stargates and Stargate Command launches an investigation to find the mythical city of Atlantis. Situated in the distant Pegasus Galaxy, it?s farther than any Stargate team has ever traveled. With only enough power to make a one-way trip, a new team, headed by civilian Dr. Elizabeth Weir (Torri Higginson), is formed and travels through the gate to this unknown galaxy. There, they discover the marvels of the lost city of Atlantis?. and encounter a sinister new enemy.
Episode 2 : Hide and Seek
Dr. Rodney McKay (David Hewlett) undergoes experimental gene therapy, altering his DNA to match the Ancient genetic coding. The experiment opens up countless scientific possibilities, as well as an unexpected problem. Meanwhile, during a game of hide and seek, one of the Athosian children inadvertently opens a containment unit that lets loose a seemingly harmless black ethereal cloud. But when Atlantis goes through a series of technical malfunctions, they realize that the shadowy creature is actually feeding off of the power supply!
Episode 3 : Thirty Eight Minutes
Fleeing from a surprise encounter with the Wraith, Major Sheppard (Joe Flanigan) falls victim to an alien symbiote which is feeding off his life force and slowly paralyzing him. While speeding back to Atlantis for medical aid, the team gets trapped halfway through the Stargate when the puddle jumper, damaged in the altercation with the Wraith, suffers a mechanical failure. With only thirty-eight minutes before the Stargate shuts down, Lieutenant Ford (Rainbow Sun Francks) and Dr. McKay (David Hewlett) struggle to manually fix the problem. As the clock ticks away, the Atlantis team must come together, or perish in the harsh vacuum of space.
Episode 4 : Suspicion
Relationships are torn part when the Athosians are accused of harbouring a spy.
Episode 5 : Childhood's End
During an exploratory mission, the puddle jumper?s electrical systems are knocked out by a massive electromagnetic field and the team is forced to make an emergency landing. They soon encounter a primitive tribe of children who have been untouched by the Wraith for centuries due to the protective force of the electromagnetic field. But the children believe it is their ritual of mandatory suicide at the age of 25 that keeps the enemy at bay, despite the contrary insistence of the Atlantis team. Fearing the ?full growns? in their midst will attract the Wraith, the villagers become anxious for their unexpected guests to leave as soon as possible. But to be able to leave, Dr. McKay (David Hewlett) must first disable the electromagnetic field. In doing so, he unwittingly trips a Wraith silent alarm, leaving the tribe open to attack.
Episode 6 : Poisoning the Well
The Atlantis team encounters the Hoffans, a human civilization in the process of rebuilding their society since the last attack of the Wraith. The resilient Hoffans have developed the beginnings of a drug that could potentially make them immune to their enemies. Fearing that the next Wraith culling will come before they are able to complete their tests, the leaders demand that their people be inoculated before the drug can be proven safe. Dr. Beckett (Paul McGillion) argues that there is no way to know what the true effects of the drug will be. Can Beckett make the Hoffans see reason, or has their haste made them blind to the epidemic they may be unleashing upon themselves?
Episode 7 : Underground
With the city's food supply dwindling, the Stargate Atlantis team must search for an alternate food source. The team begins negotiation with a simple group of farmers known as the Genii. Untrusting of outsiders, the Genii are hesitant to any sort of trading?until Major Sheppard (Joe Flanigan) demonstrates the team's advanced weaponry. A deal is struck to exchange food for explosives. But upon returning to the Genii village to make the exchange, they stumble upon technology that leads them to believe the Genii are not at all what they seem.
Episode 8 : Home
During an exploration of a planet with no apparent inhabitants, Dr. McKay (David Hewlett) discovers that the planet's fog-like atmosphere is actually pure energy? enough to open a wormhole back to earth. Wanting to be sure they could return to Atlantis to continue their mission, Dr. Weir (Torri Higginson) relays a message back to Stargate Command. They are told that the battleship Prometheus has been outfitted with a hyperdrive and they would be able to return to Atlantis within a month! Back on Earth, the team is overjoyed to be with the things and people they love. However, when the Prometheus' hyperdrive is accidentally destroyed, their hopes of ever returning to Atlantis are suddenly dashed.
Episode 9 : The Storm
The team learns that a storm of catastrophic proportions is headed straight for the city of Atlantis. Without enough energy to power the shields, Dr. Weir (Torri Higginson) orders that Atlantis be evacuated until the storm passes. But Dr. McKay (David Hewlett) conceives of a last minute plan to save the city ? harness the power of the electrical storm to fuel the shields. Meanwhile, unbeknownst to the Atlantis team, the Genii have learned of Atlantis? evacuation, and devise a dangerous plan to take over the city?s weapons for themselves. With Weir and McKay taken hostage and Lt. Ford (Rainbow Sun Francks) and Teyla (Rachel Luttrell) aiding the evacuees, it is up to Major Sheppard (Joe Flanigan) to shut down the remaining grounding stations and save Atlantis from invasion before the storm hits.
Episode 10 : The Eye
As the storm approaches, Commander Kolya of the Genii, who has seized Atlantis, is about to shoot Dr. Weir. Suddenly, Dr. Rodney McKay steps in front of the gun and convinces Kolya that he and Weir are the only ones who can fix Grounding Station 3, the last of the four grounding stations that must be disabled so that lightning from the storm can be channeled into the shield generator, to power up the shield and protect Atlantis from being obliterated. Kolya spares their lives, but contacts Maj. John Sheppard over the radio and tells him that Weir is dead. Sheppard vows to kill Kolya. Meanwhile, on the mainland, Lt. Aiden Ford, Teyla and Dr. Carson Beckett are waiting out the storm in a Puddle Jumper. Suddenly, the wind stops and the sky clears. They are in the eye of the storm. Ford commands a reluctant and frightened Beckett to fly the Puddle Jumper straight up the eye, over the storm to Atlantis to help Sheppard. On Atlantis, a female Genii named Sora reports to Kolya that Sheppard has killed three more of their men. Weir and McKay, who are working to bypass the broken switch on the grounding station, overhear the conversation and try to stall the repair to give Sheppard more time. Kolya commands Sora to radio Chief Cowen, leader of the Genii, to send a full company of 60 men through the stargate, dashing Weir and McKay's hopes of rescue. Atlantis is powered by five small Naquadah generators, each responsible for a separate area of the city. Two of the generator rooms are conveniently located near transporter stations. Sheppard disables the generators powering stargate operations and Grounding Station 3, making it impossible for McKay and Weir to finish their task. Sheppard then storms the control room and raises the 'gate shield. Only five of Kolya's 60 men get through. The rest are destroyed by the shield. The storm is less than an hour away. Kolya radios Sheppard with a proposition. If Sheppard doesn't restore power to Grounding Station 3 in the next 10 minutes, Weir really will be killed, followed by McKay 10 minutes later. Sheppard, relieved to hear Weir's voice, has no choice. Joined by Ford, Teyla and Beckett, he restores power to Grounding Station 3. McKay is disables the station. In the control room, Kolya orders McKay to power up the shield. McKay and Weir bluff Kolya into believing that McKay's plan has failed and that Atlantis is lost. He decides to withdraw, but also to take Weir and McKay with him. Sheppard and Ford storm the control room and take out Kolya's remaining men. Kolya uses Weir as a human shield and backs toward the activated stargate. Sheppard takes the shot and hits Kolya, who releases Weir as he falls backward through the 'gate. With the storm due to hit in 2.5 minutes, Teyla and Beckett are unaccounted for. That's because Sora has knocked Beckett unconscious and is fighting Teyla, whom she believes to be responsible for her father's death. Teyla wins but lets Sora live. Sora follows Teyla, who drags Beckett to the control room. Weir gives McKay the order. Lightning strikes Atlantis and floods the corridors. The shield activates just before a huge wave hits the city. Atlantis is saved and Weir orders Sora held as a prisoner.
Episode 11 : The Defiant One
Leading an exploration of an ancient weapons satellite in deep space, Major Sheppard (Joe Flanigan) and Dr. McKay (David Hewlett) intercept a Wraith distress signal. Deciding to investigate, the team lands on a nearby planet and finds the source of the call - a downed Wraith cargo ship. When the unseen Wraith awakens from hibernation, Sheppard and McKay become the focus of its ravenous appetite.
Episode 12 : Hot Zone
While assessing the structural damage to the city caused by a massive storm, two of Dr. McKay?s (David Hewlett) team of scientists experience horrifying visions. Minutes later, they drop dead. Retracing the steps of the dead scientists, McKay and his team find an Ancient lab, its contents in disarray. Afraid of a viral outbreak, Dr. Weir (Torri Higginson) places the city under a self-regulated quarantine. Even with the city under lockdown under the threat of a possible viral outbreak, more and more people begin suffering from the same terrifying visions. If McKay cannot find a cure, the entire city will be doomed.
Episode 13 : Sanctuary
Engaged in combat, the Atlantis team?s puddle jumper is hit with an energy wave that leaves them unharmed, but destroys their Wraith attackers. Hoping to find the source of the wave, the team lands on the planet below. There they find a civilization enjoying the utmost health and happiness, untouched by the Wraith. Their leader, Chaya, refuses to allow anyone other than her own people the sanctuary and safety from the Wraith that would be found by settling on their planet. Unwilling to give up so easily, Major Sheppard (Joe Flanigan) asks Chaya to reconsider. After thinking it over, Chaya surprises everyone by requesting to accompany them back to Atlantis to discuss the matter further leading the team to suspect they may be caught in a trap.
Episode 14 : Before I Sleep
While exploring the city, the Atlantis team discovers a stasis chamber holding a woman who appears to be over 10,000 years old. Excited at the possibility that she is one of the Ancients, the alien race that built Atlantis, the team decides to bring her out of stasis despite the risk to her health. Everyone is shocked when, once re-animated, the elderly woman identifies herself as none other than Dr. Weir (Torri Higginson).
Episode 15 : The Brotherhood
The Atlantis team travels to Dagan, a planet with a hidden ZPM and a mysterious trail that will lead to its hidden secret chamber location. But the Genii have learned of the Atlantis team?s activities on Dagan. Realizing the ZPM must hold awesome power, the Genii plant a sleeper agent amongst the Daganians aiding the Atlantis team on their search. Now, as the Atlantis team closes in on the location of the ZPM, the Genii close in on them.
Episode 16 : Letters from Pegasus
Having learned that the entire Wraith armada is headed towards the city, the Atlantis team prepares to send a data message to Earth with information about the Wraith threat, and what could be their last messages home to loved ones. As the rest of the team records their touching and often humourous messages back home, Major Sheppard (Joe Flanigan) and Teyla (Rachel Luttrell) embark on a reconnaissance mission where they witness the vastness of the Wraith army, and look on helplessly as the Wraith cull the planet?s helpless inhabitants.
Episode 17 : The Gift
Terrifying nightmares about the Wraith cause Teyla (Rachel Luttrell) to lash out at her colleagues and prompt her to seek professional advice. With psychological guidance, she discovers that she can sense the Wraith. In their search to learn more, Teyla and the Atlantis team discover important information that may hold the key to understanding their enemy, including the disturbing possibility that Teyla?s connection to the Wraith could be the result of genetic experimentation.
Episode 18 : The Siege, Pt. 1
With the Wraith armada closing in on Atlantis, Dr. McKay (David Hewlett) and a small team attempt to repair an ancient weapons satellite in the hopes of leveling the odds in the coming battle. Meanwhile, tension builds between Teyla and some of the other members of the Atlantis team over her connection to the Wraith. Major Sheppard (Joe Flanigan) steps in to defend her, but even he begins to harbour doubts when a team member is left unconscious after an attack by an unknown assailant.
Episode 19 : The Siege, Pt. 2
With the Wraith armada bearing down on the city, the Atlantis team prepares to evacuate. Setting the city?s self-destruct sequence, they hope to make it impossible for the Wraith to gain access to Earth. Things begin to look up when reinforcements from Earth are brought in and it is announced that the battleship Daedalus will arrive in four days. However when the warheads are easily destroyed by the Wraith, and the first wave of Wraith attackers strafe the city with weapons fire, it becomes increasingly clear that the added reinforcements are not going to be enough. With time running out, the Atlantis team must turn to the least likely source of aid ? the duplicitous Genii! But with the Wraith overrunning the city, even the Genii?s help may not be enough.