When Rodney McKay 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 leads a group of Atlantis personnel on a desperate jumper mission to clear a path for the city. Meanwhile Dr. Keller’s attempts to resuscitate a comatose Elizabeth Weir 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.

Lt. Col. Sheppard 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.Directed by Weir and McKay from the jumper, Sheppard and Ronon 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, aboard the Apollo, searches in vain for the missing city.

On an off-world village Ronon and Teyla discover a group of warriors from Ronon’s homeworld, Sateda. These Satedans, led by Tyre have a plan to infiltrate a Wraith weapons facility but need the Atlanteans help to do it. Meanwhile, Col. Samantha Carter 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 and his team come under fire from the Wraith. Ronon escapes but Sheppard and company are captured. The Wraith force McKay 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.

While Lt. Col. Sheppard 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 is the first to experience a nightmare involving Sheppard. The chain reaction continues when she infects Dr. Keller , who succumbs to a different but equally terrifying dream. When Lorne appears to have a psychotic breakdown, the team urgently attempts to trace the problem to its source. When Rodney McKay 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.

Ambushed and imprisoned aboard a rogue human-run ship, Lt. Col. Sheppard is threatened with death by its attractive female commander, Larrin , 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.

After working for countless hours on the Replicator coding, Dr. McKay 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. 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 and Ronon to figure out who has stolen the Replicator information…and the only two people who have the knowledge to understand it.

As Dr. Rodney McKay 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, Teyla and Ronan 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.

High above the Replicator home world, 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.

A nervous Dr. McKay arrives in the botany lab with the intention of asking Katie to marry him when an alarm sounds throughout the city. It immediately activates a quarantine shut down, trapping them in the lab with no way out. McKay suspects that either a highly infectious disease has triggered the city’s automatic self-protection system, or he may have gone overboard with his efficiency upgrades. But help is not imminent. Lt. Colonel Sheppard and Teyla have been simultaneously locked in McKay’s lab, Colonel Carter and Dr. Zelenka are confined in the transporter, and Dr. Keller and Ronan are stuck in the infirmary. With communications and other vital systems affected, each believes the other will be coming to their rescue, unaware that they all share the same predicament.

While re-visiting an off-world trading partner, Lt. Colonel Sheppard and Dr. McKay receive high praise from the beautiful princesses Mardola and Flora 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, 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 soon 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.

When Lt. Colonel John Sheppard is informed that his father has passed away he packs a few things and, accompanied by Ronan, 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.

Disheartened by another unsuccessful search for Teyla, Lt. Colonel Sheppard 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.