Episode 1 : Adrift
When Rodney McKay (David Hewlett) realizes Atlantis has started shutting down artificial gravity and collapsing protective shields to compensate for a damaged power system, he turns off all non-essential systems. But when the problem persists, McKay is forced to collapse the shield to the point where it is only protecting Atlantis' main tower, leaving the rest of the city exposed to space.With the protective shields down and an asteroid belt fast approaching, Lt. Col. Sheppard (Joe Flanigan) leads a group of Atlantis personnel on a desperate jumper mission to clear a path for the city. Meanwhile Dr. Keller's (Jewel Staite) attempts to resuscitate a comatose Elizabeth Weir (Torri Higginson) reveal that her patient has severe brain swelling and will require radical surgery. McKay runs the calculations and realizes there's an even bigger problem: in just 28 hours, the city's shields will fail completely and all of Atlantis' inhabitants will succumb the vacuum of space.
Episode 2 : Lifeline
Lt. Col. Sheppard (Joe Flanigan) leads his team on a daring raid on the Replicator home world in a bid to secure a ZPM that will save Atlantis. The key to their operation is none other than Dr. Elizabeth Weir (Torri Higginson). Directed by Weir and McKay (David Hewlett) from the jumper, Sheppard and Ronon (Jason Momoa) head deep into the Replicator city to acquire the sought after prize. But a surprising revelation concerning a long-dormant Replicator sub-routine changes the plan, forcing Sheppard and company to forego their quick escape. When the Replicators become aware of the incursion, Sheppard's team must keep them at bay or else abandon the mission and their hope of saving Atlantis. Meanwhile Colonel Carter (Amanda Tapping), aboard the Apollo, searches in vain for the missing city.
Episode 3 : Reunion
On an off-world village Ronon (Jason Momoa) and Teyla (Rachel Luttrell) discover a group of warriors from Ronon?s homeworld, Sateda. These Satedans, led by Tyre (Mark Dacascos), have a plan to infiltrate a Wraith weapons facility but need the Atlanteans help to do it. Meanwhile, Col. Samantha Carter (Amanda Tapping) arrives on Atlantis as the new leader, and her first task is to execute new security protocols that leave Ronon feeling alienated and considering leaving Atlantis for good. Once inside the Wraith weapons facility, the two teams split up, and Sheppard (Joe Flanigan) and his team come under fire from the Wraith. Ronon escapes but Sheppard and company are captured. The Wraith force McKay (David Hewlett) to make changes to the Replicator base code using an actual Replicator the Wraith have imprisoned in the facility. Ronon and Carter mount a rescue operation, and, in the end, Ronon learns the truth about his old friends' new loyalties.
Episode 4 : Doppelganger
While Lt. Col. Sheppard (Joe Flanigan) and the team are out exploring a jungle planet, they discover a glowing crystalline growth. Compelled to touch the strange crystal, Sheppard becomes host to an alien entity. Once on Atlantis, the entity begins to move from person to person through the power of touch. Teyla (Rachel Luttrell) is the first to experience a nightmare involving Sheppard. The chain reaction continues when she infects Dr. Keller (Jewel Staite), who succumbs to a different but equally terrifying dream. When Lorne (Kavan Smith) appears to have a psychotic breakdown, the team urgently attempts to trace the problem to its source. When Rodney McKay (David Hewlett) becomes the latest host, the team links Sheppard to McKay's brain, where Sheppard ultimately faces off against the malevolent entity that has assumed his form.
Episode 5 : Travelers
Ambushed and imprisoned aboard a rogue human-run ship, Lt. Col. Sheppard (Joe Flanigan) is threatened with death by its attractive female commander, Larrin (Jill Wagner), unless he helps her reactivate a dormant Lantean spaceship. A nomadic group of travelers live on this rundown vessel, part of a greater armada, and their need for new ships has become critical. As soon as Sheppard steps aboard, he discovers that the Lantean ship, abandoned after an attack by the Wraith, is now emitting deadly radiation. Unbeknownst to Larrin, Sheppard manages to send out a sub-space distress signal - but the signal attracts a Wraith cruiser. As the team searches for him, Sheppard's resourcefulness is put to the test as he tries to stay alive, with or without Larrin's help.
Episode 6 : Tabula Rasa
Plant samples brought back from a new planet introduce an amnesia-inducing virus that strikes everyone in the city except Teyla (Rachel Luttrell) and Ronon (Jason Momoa), who appear to be immune. Carter (Amanda Tapping) orders the Gate?s control crystal removed to stop the disease from spreading to other planets while Major Lorne (Kavan Smith) and his soldiers are given orders to control the Atlantis population with stun guns. The team discovers that a cure might be available among the plants on the mainland, so Ronon and Sheppard (Joe Flanigan), whose memory is also fading, set off to obtain it. Meanwhile, McKay (David Hewlett) works on a widespread distribution method but is unable to complete it before he too succumbs to the virus. When McKay wakes up, he is strapped to his desk in front of his console, with no idea who he is or what is going on. Following instructions from a video he recorded earlier, McKay frees himself and sets out to find Teyla (Rachel Luttrell), the key to unlocking this mystery.
Episode 7 : Missing
Teyla (Rachel Luttrell) is shocked to find the Athosian settlement on New Athos completely deserted when she and Dr. Keller (Jewel Staite) arrive for a visit. Upon encountering the menacing Bola Kai, a fierce warrior tribe, the two women flee for their lives into the surrounding forest. Virtually weaponless and slowed by Keller, who has injured her ankle, the pair must avoid capture by the Bola Kai until their failure to return alerts Atlantis to send a search party. Keller and Teyla find a bound and wounded man named Nabel (Johann Hels), who claims that Teyla's people were culled by the Wraith. Ultimately, the three are captured, and the Bola Kai's tribe leader Omal (Danny Trejo) threatens to kill them unless they betray the location of Atlantis.
Episode 8 : The Seer
With still no trace of the Athosians, Teyla (Rachel Luttrell) requests an off-world visit to meet with a seer, Davos (Martin Jarvis), who may be able to help her find her people. After convincing even McKay (David Hewlett), the most skeptical of the team, of his psychic abilities, an ailing Davos travels back to Atlantis to receive medical treatment. While there, he has visions of tragic and devastating consequences for Atlantis. Meanwhile, the Wraith bring a startling proposal to Lt. Col. Sheppard (Joe Flanigan) along with information that the Replicators are finding new ways to destroy human civilizations throughout the galaxy with devastating results. The only way to stall their attacks may be to collaborate with the Wraith in a dangerous partnership. Adding to the stress on Atlantis is the arrival of Agent Woolsey (Robert Picardo) who has been assigned to observe and review Col. Carter (Amanda Tapping) in her newly appointed position as leader of the city.
Episode 9 : Miller's Crossing
After working for countless hours on the Replicator coding, Dr. McKay (David Hewlett) reluctantly admits that he needs help with the program. And the only available person who can match - or exceed - his knowledge is his sister Jeanie (Kate Hewlett). After working on the calculations from Earth, Jeanie sends her results back to Atlantis and heads to bed. But the calm is broken when her bedroom is stormed by four men, wielding MP-5's, who tie up her husband and drag Jeanie into the night. When news reaches Atlantis that his sister is missing, McKay travels to Earth racked by guilt for involving his sister. He is determined to find her and uncover who is behind the kidnapping. But when McKay also goes missing, it's up to Lt. Col. Sheppard (Joe Flanigan) and Ronon (Jason Momoa) to figure out who has stolen the Replicator information... and the only two people who have the knowledge to understand it.
Episode 10 : This Mortal Coil
As Dr. Rodney McKay (David Hewlett) struggles to figure out why the stargate has been inoperable for over a week, a mysterious probe plunges into the city. A subsequent decryption sweep of the probe offers McKay a shocking glimpse of nanite code before his diagnostic program crashes and all the data is lost. Meanwhile, Lt. Col. Sheppard (Joe Flanigan), Teyla (Rachel Luttrell) and Ronan (Jason Momoa) have noticed that the some of the crew are behaving oddly. The mystery deepens still further when a former member of the expedition is discovered lying unconscious in a hidden room. Convinced that the replicators have finally found their location, the team grapples with these implications, unaware that their problems may very well be insurmountable.
Episode 11 : Be All My Sins Remember'd
The Replicators remain undeterred in their effort to wipe out the Wraith's human food supplies, but the Atlantis team is now armed with the means to track their ships. With time in short supply, Sheppard (Joe Flanigan), Teyla (Rachel Luttrell) and Ronan (Jason Momoa) rush to evacuate those human settlements which lie in the path of the advancing Replicator forces. Meanwhile, both Colonel Caldwell (Mitch Pileggi), commander of the Daedalus and Colonel Ellis (Michael Beach), commander of the Apollo, arrive from Earth. Each is in possession of Asgard based weaponry, ready to confront an armada of Replicator ships. But Dr. McKay (David Hewlett) is not convinced that this is the best offensive and, in partnership with a wraith scientist, struggles to create a program that will effectively shut down the replicators for good. But the team's best laid plans are fraught with hurdles, further fuelled by an unexpected appearance from Larrin (Jill Wagner), the leader of a race of space travelers not unknown to Sheppard.
Episode 12 : Spoils of War
High above the Replicator homeworld, a provisional alliance wages an all-out assault on the Replicator fleet. As the battle wages, a group of wraith execute a last-minute plot to retrieve a ZPM from the planet's surface. Weeks later, the Atlantis long-range sensors detect the signal of a subspace tracking device familiar to Dr. McKay. The team follows to signal to a damaged hive ship drifting in space. Amidst the ship's records, they discover references to a secret wraith base...
Episode 13 : Quarantine
A nervous Dr. McKay (David Hewlett) arrives in the botany lab, prepared to pop the question and finally ask Katie to marry him when an alarm sounds throughout the city. A quarantine lockdown goes into effect, trapping them in the lab. McKay suspects that a highly infectious disease has triggered the city's automatic self-protection system.
Episode 14 : Harmony
While re-visiting an off-world trading partner, Lt. Colonel Sheppard (Joe Flanigan) and Dr. McKay (David Hewlett) receive high praise from the beautiful princesses Mardola (Crystal Lowe) and Flora (Anna Van Hooft) who express their undying gratitude for the trade, medical assistance and protection Atlantis has provided for the past several years. The princesses beg a further favor, asking Sheppard and McKay to accompany their sister Harmony (Jodelle Ferland), designated successor to the throne, to the ruins of the Temple of Laros, a mandatory rite of passage. Reluctant to jeopardize their otherwise untroubled alliance and anticipating that the third sister will be equally beguiling, Sheppard and McKay agree to escort Harmony on a journey promised to take no longer than a day. Their chivalry is challenged upon meeting Harmony, a thirteen year old child with high expectations of her protectors. Disheartened, Sheppard and McKay nonetheless proceed with their mission, unaware that she has enemies, and character flaws, yet to be dealt with.
Episode 15 : Outcast
When Lt. Colonel John Sheppard (Joe Flanigan) is informed that his father has passed away he packs a few things and, accompanied by Ronan (Jason Momoa), heads back to Earth to attend the funeral. There, Ronan gains some insights to his friend's past - Sheppard's troubled relationship with his father and brother, as well as his ex-wife Nancy, a director with Homeland Security. Before long, they are approached by a woman, Ava Dixon, who claims to know about a covert project involving nanite programming. Sheppard's worst fears are realized when she leads them to a high tech lab and reveals that she and her partner have been successful in creating a human form Replicator - a Replicator now loose somewhere in the city who must be recaptured at all cost.
Episode 16 : Trio
Col. Samantha Carter (Amanda Tapping) joins Dr. McKay (David Hewlett) and Dr. Keller (Jewel Staite) on a mission to convince the inhabitants of an off-world village rocked by frequent tremors, to move to a more stable part of the continent. But en route to the village, Dr. McKay plunges into a sinkhole, falling twenty feet to the bottom of a large subterranean chamber. Crawling to the edge of the rupture, Carter and Dr. Keller are relieved to see that McKay is unhurt. Suddenly, they feel the ground beneath them give way and they too drop out of sight. Realizing that they have fallen into a section of an old Genii mining facility they begin to search for a way out. But every attempt to escape the confines of the chamber seems to put them in further jeopardy, underscored by the constant tremors that shake their prison with ever greater force.
Episode 17 : Midway
Mr. Coolidge is the newest member of the IOA and openly distrustful of alien participation in any facet of the Stargate program. Despite his bias, the IOA has entrusted him with interviewing Teyla Emmagan (Rachel Luttrell) and Ronan Dex (Jason Momoa) about their suitability to continue as members of the Atlantis expedition. This does not bode well for Ronan who is next on the list to travel to Earth for questioning. Colonel Carter (Amanda Tapping), concerned that Ronan's temper will explode under intense cross-examination, asks an old friend to travel to Atlantis to serve as his mentor - Teal'c, of the Jaffa. But Ronan, insulted by the implication that he can't handle himself, makes no effort to befriend Teal'c and their stay on the Midway station, en route to Earth, does little to improve the situation. Unbeknownst to anyone, a plan by the Wraith to invade the Midway station is about to be initiated, and an interview with Mr. Coolidge will be the very least of their problems.
Episode 18 : The Kindred, Pt. 1
Dr. Keller (Jewel Staite) is perplexed by a mysterious new sickness that has affected a number of planets in the Pegasus Galaxy and threatens to kill hundreds of thousands of people. Further study reveals that it is not a contagion but a human engineered protein designed to kill a feeding wraith. Col. Carter (Amanda Tapping) and Dr. Keller realize that someone is intentionally infecting the Wraith's food supplies with no concern for the thousands of human carriers who are dying in the process. Meanwhile, Teyla (Rachel Luttrell) shares with Dr. McKay (David Hewlett) a vision she had in which Kanaan, the father of her child, was trying to send her a message that he is still alive. Now, more determined than ever to find him and the other missing Athosians, she convinces Sheppard (Joe Flanigan) to travel with her to a trading settlement in search for answers. What they find there leads them to startling discovery that no one could have anticipated.
Episode 19 : The Kindred, Pt. 2
Everyone on Atlantis is surprised to learn that a friend, once thought dead, is miraculously back among them. A captive Teyla (Rachel Luttrell), meanwhile, is re-united with her missing fellow Athosians who have also been interned at one of Michael's secret facilities. Ever hopeful that Sheppard (Joe Flanigan) will be able to mount a rescue, she begins to formulate a plan to ensure their escape, if he is able to find them in time.
Episode 20 : The Last Man
Disheartened by another unsuccessful search for Teyla, Lt. Colonel Sheppard (Joe Flanigan) returns home to Atlantis and immediately senses that something is not right. Further investigation reveals that not only has the city been completely abandoned, its systems are all dead and, instead of ocean, is now surrounded by rolling sand dunes as far as the eye can see. A significantly older looking McKay appears - a hologram with devastating news to relay. A freak anomaly has sent Sheppard over forty thousand years into the future and everyone he has ever known is long dead. But McKay has a risky plan to return Sheppard to the past, and reverse a future that went horribly wrong.