With a damaged ZPM, and diminished hopes of survival, the Atlantis team finds themselves stranded in the middle of empty space with hardly any time before they run out of power completely. Dr. McKay is challenged to the max as he tries to find a way to save Atlantis from its doom. Meanwhile, Dr. Keller races to treat Weir's increasing head injuries, but the only answer she can come up with could have grave results for everyone on board.
The Atlantis team, along with Weir and now with the ability to make large hyperspace jumps in only a puddle jumper, must now journey to the replicator home planet to steal one of their many ZPMs to bring the city back to life, and finish the journey to their new planet
While on a regular mission, Ronan runs into some Satedan friends from his past. As old emotions start to return, new thoughts come with them, one of which involves leaving Atlantis. But could danger be lurking just around the corner?
While exploring a new planet, Sheppard started to watch a strange crystal. He doesn't know why, but he had to touch it. Back on Atlantis, everybody but him started to have some bad nightmares.
Sheppard is kidnapped by a group of people living in a starship fleet. They were telling him that they were living on these ships for a long time, due to the war with the Wraith. He was forced to help them make an ancient's ship fly. Sheppard tricked them and flew with the ship, and 3 of the kidnappers.
Dr. McKay is in a lab in Atlantis, and he doesn't know where he is, or who he is. There's a computer next to him, with a message telling him to find Teyla; she's the only one who can save them all. McKay is chased by a group of soldiers, led by Major Lorne.
Teyla and Dr. Keller go to the Athosian's new planet, and what they see is that the Athosian are not there anymore. They've gone missing. It seems to be the work of a warrior tribe, the Bola Kai.
The team meets a man with extraordinary prophetic abilities, who gives them a dark prediction about Atlantis' future. Meanwhile, they join forces with a Wraith in an attempt to fix the virus Rodney created earlier to stop the Replicators, that has since malfunctioned. And Woolsey arrives at Atlantis to conduct an evaluation of Carter's command.
McKay and his sister are kidnapped on Earth by a man in need of their expertise. The rest of the Atlantis team must enlist the help of an NID agent to rescue them.
When what appears to be a satellite crashes into Atlantis, the team becomes aware of strange behaviour on the base.
The Atlantis team decides to attack the numerous ships of the Replicators, with the help of uneasy alliances.
A transmission from space leads the team to the discovery of a breeding ground for Wraith soldiers.
The entire city locks down for a false quarantine, leaving people stranded with a decreasing amount of oxygen, while Rodney is unable to reach a computer.
Sheppard and McKay must escort a prospective queen as part of their diplomatic duties, unaware that an ambush has been set by some familiar enemies.
After returning to Earth for his father's funeral, John Sheppard discovers the existence of a human form Replicator loose on the population.
Keller, Carter and McKay are stranded in an abandoned Genii mine while off-world.
When Colonel Carter invites Teal'c to Atlantis to counsel Ronon, who is up for review by the I.O.A., word comes in that the Wraith have discovered the now fully operational Midway Space Station.
While a disease spreads through the Pegasus Galaxy, Teyla believes the father of her child is trying to communicate with her. While searching for answers, the team comes across a very interesting discovery.
After finding some of the missing Athosians, Teyla plans an escape from Michael's secret facility. Meanwhile, Keller investigates the origins of the Beckett duplicate.
Sheppard returns from a mission and finds Atlantis abandoned and surrounded by sand dunes. He soon finds a hologram of Dr. McKay, who tells him he has come 48,000
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