McKay finds a way to send a message to Earth, leaving space for personal messages. Sheppard and Teyla are off to spy on the Wraith fleet approaching Atlantis.

McKay and a pilot crash with a puddle jumper into the ocean on Atlantis. They start to sink.

Rodney's sister is brought to Atlantis to make use of one of her theories.

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 Ancients ship fly. Sheppard tricked them and flew with the ship, and 3 of the kidnappers.

Rodney McKay awakens in his lab, tied to a chair and with no memory of who or where he is. He did seemingly leave himself a video message telling him to look for Teyla. The problem began some 14 hours before when Dr. Katie Brown returned to Atlantis with plants from a planet she had visited. The plants had been cleared through the normal quarantine procedure but she is soon afflicted with severe headaches and loss of memory, eventually falling into a coma. Memory loss begins to afflict other members of the crew but they soon become distrustful of one another, making conclusions based on false assumptions and a misreading of the situation. Fortunately, there are two members of the team who seem to be immune.

Teyla and Dr. Keller go to the Athosians' new planet, where they discover that the Athosians have gone missing. It seems to be the work of a warrior tribe, the Bola Kai.

Having been told by the Genii spy on New Athos that her people were still alive, Teyla asks permission to visit a man named Davos who is a legendary seer and may be able to help her. When they arrive, Dr. Keller realizes that the man is dying. His ability to see the future is real, but the snippets of the future he is able to show them are open to interpretation. John is called back to Atlantis when they receive a message from the Wraith whose life he had previously saved. He offers to work with McKay to fix the nano virus that is now malfunctioning. As if this weren't enough happening, Richard Woolsey arrives from Earth to undertake Samantha Carter's 3 month evaluation.

When McKay's sister Jeanie is kidnapped, the team returns to Earth to find her.

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.

The IOA is conducting interviews back on Earth to ensure that any personnel serving on Atlantis (in particular, aliens) are suitable for their roles. The episode opens up with a pregnant Teyla having been interviewed and reporting back to Atlantis. Ronon is next. Col. Carter is unsure about Ronon's ability to handle the IOA's interview and therefore asks Teal'c to come to Atlantis in a coaching capacity for Ronon. After a rocky start to their relationship, Ronon and Teal'c return to Earth, via the series of Stargates and a Midway Station, that McKay had previously designed. The Midway Station between the Milky Way and Pegasus galaxies serves primarily as a place for those traveling between the galaxies to serve a 24 hour quarantine. While Teal'c and Ronon are serving their quarantine in the extremely cramped Midway Station, it is boarded by the Wraith, via the Stargate, with the intention to travel to Stargate Command on Earth. They achieve this objective, but only with Teal'c and Ronon in tow. What ensues is a battle between the Wraith and the duo of Teal'c and Ronon, for control of Stargate Command.

A plague of sorts is spreading across the Pegasus galaxy and Dr. Keller estimates that hundreds of thousands will die if they don't don't find a way to stop it. Her research shows however that the disease's origin is with the Hoff, who had been working on a way to kill the Wraith. Sheppard and the others think they know who might be spreading the virus and why. Teyla meanwhile believes she is receiving messages from Kanaan, the father of her child. She's getting his messages while sleeping and most think she's just dreaming. She follows the clues he gives her but she is taken prisoner by an old enemy who has very specific plans for her. In their search for Teyla however, Sheppard and McKay find someone completely unexpected.

Slowly, everyone on Atlantis comes to terms with the sudden re-appearance of Dr. Carson Beckett who, he claims, has been Michael's prisoner for some two years. He tells them what he was doing in Michael's laboratory and they set off to find the kidnapped Teyla. Dr. Keller figures out just how he's come to there at all. Sheppard meanwhile has been using all of his contacts to try and locate Teyla but they come across someone from the past. Teyla in turn has found some of the Athosians alive but they are few in number as a result of Michael's experiments. Michael explains to her just what it is he wants from her as well as his own plans for the future.

After yet another fruitless search for the missing Teyla, Sheppard returns to Atlantis, only to find it deserted. Worse yet, the city isn't just abnormally hot, but the entire ocean has completely dried up, leaving a sandy desert! Sheppard then finds a hologram of an aged Dr. McKay, telling him that a solar flare had sent him 48,000 years into the future. Once he learns the demise of Atlantis and everyone on it, and worse yet that the sun in the solar system is dying and he won't survive there much longer, he and the holographic McKay must find a way to send Sheppard home and potentially change all of this.

Combat engineers from Atlantis work against the clock to rescue four of their colleagues who are now trapped in the rubble of Michael's medical compound. With Michael en route, they quickly locate McKay and Major Lorne but Sheppard and Ronon are far deeper and their rescue is not assured. When Michael's ship arrives, they decide to try to rescue Teyla who is in labor and close to giving birth. When it's all over, Col. Carter is recalled to Earth for a performance review but Richard Woolsey has some bad news for her.

Sheppard and his team are lured to a planet and are soon put on trial for crimes against the people of the Pegasus galaxy. In flashbacks, the three judge tribunal recounts the indictment against them including the re-awakening of the Wraith and the various missions where at least a few, if not more, innocent bystanders were killed. Sheppard does his best to argue that on balance, fewer were killed by their presence than would have been the case if they had never been there. A least one of the judges is clearly determined to find them guilty while a second seems far more sympathetic. It's left to Richard Woolsey, who has now joined them, to plead the rest of their case. A lawyer by profession, Richard clearly knows how the game is played and focuses on that third judge.

A hive ship turbo-charged with a ZPM has received the Wraith's message from a alternate universe containing the location of Earth. The ship is now heading for Earth.

Having been told by the Genii spy on New Athos that her people were still alive, Teyla asks permission to visit a man named Davos who is a legendary seer and may be able to help her. When they arrive, Dr. Keller realizes that the man is dying. His ability to see the future is real, but the snippets of the future he is able to show them are open to interpretation. John is called back to Atlantis when they receive a message from the Wraith whose life he had previously saved. He offers to work with McKay to fix the nano virus that is now malfunctioning. As if this weren't enough happening, Richard Woolsey arrives from Earth to undertake Samantha Carter's 3 month evaluation.

McKay and a pilot crash with a puddle jumper into the ocean on Atlantis. They start to sink.

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?

Combat engineers from Atlantis work against the clock to rescue four of their colleagues who are now trapped in the rubble of Michael's medical compound. With Michael en route, they quickly locate McKay and Major Lorne but Sheppard and Ronon are far deeper and their rescue is not assured. When Michael's ship arrives, they decide to try to rescue Teyla who is in labor and close to giving birth. When it's all over, Col. Carter is recalled to Earth for a performance review but Richard Woolsey has some bad news for her.

Keller, Carter and McKay are stranded in an abandoned Genii mine while off-world.

The Atlantis team decides to attack the numerous ships of the Replicators, with the help of uneasy alliances.

Rodney's sister is brought to Atlantis to make use of one of her theories.

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.

After yet another fruitless search for the missing Teyla, Sheppard returns to Atlantis, only to find it deserted. Worse yet, the city isn't just abnormally hot, but the entire ocean has completely dried up, leaving a sandy desert! Sheppard then finds a hologram of an aged Dr. McKay, telling him that a solar flare had sent him 48,000 years into the future. Once he learns the demise of Atlantis and everyone on it, and worse yet that the sun in the solar system is dying and he won't survive there much longer, he and the holographic McKay must find a way to send Sheppard home and potentially change all of this.

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.