A team of scientists think they have found the location of the long lost city of Atlantis. It can be reached by a Stargate address that leads to the Pegasus galaxy.

Rodney can't remove an Ancient device that makes him invincible but prevents him from eating or drinking. Meanwhile, there are power malfunctions throughout the city and one of the Athosians mentions seeing a shadow.

Sheppard gets bitten by a Wraith-like bug and is dying. While the puddle jumper returns, it gets stuck in the Stargate. There's 38 minutes to find a solution.

There's suspicion of a Wraith collaborator and some of the team suspect the Athosians. Ford and Sheppard find land on Atlantis' planet.

McKay and Zelenka come up with a plan to repair the Ancients' weapon satellite. Bates and Teyla get into a fight. He is found unconscious and badly injured shortly afterwards.

Fallen into the Wraith trap, McKay initially resigns to fatal captivity in a cocoon, but Ronon keeps struggling to attempt escaping, or at least taking some Wraith down with them. Sheppard managed to hide his glider on the very hive ship, seeking a way out, surprised to get radio contact with Michael, who seeks revenge after the ingrate queen has him semi-restrained as 'too human' suspect. While they try to sabotage the hive and maybe escape, the Daedalus and Orion race just in time to fight the two hive ships before they may attack earth. Weir is summoned to SGC for a pointless grilling by the International Oversight Advisory, finding them bureaucrats unable to risk a decision beyond questioning what was already done. So she returns, never mind the career risk compared to a Wraith culling. Sheppard manages to reach the Daedalus and his party comes up with a daring plan to overpower the hive with the weaponized retrovirus, despite bombarded damage compromising even their life-support systems.

Sheppard and the others are now in control of the one remaining hive ship with most of the Wraith transformed into human form, courtesy of the retrovirus. They do learn something interesting about female Wraiths, however. After they return to Atlantis, the question becomes one of what to do with the Wraiths who are again human, especially Michael who has proved to be quite helpful. Elizabeth Weir meanwhile is surprised to hear that she is to return to Atlantis as the expedition leader. She will be accompanied however by Richard Woolsey who is to review her leadership and make recommendations to the International Oversight Advisory on whether she should be allowed to continue.

John Sheppard is kidnapped by the Genii and is in the company of a Wraith.

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?

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.

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.

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.

Teyla risks her life on a daring mission aboard a wraith hive ship.

Dr. Daniel Jackson comes to Atlantis in search of a lost Atlantian room. The discovery reveals a new race. Daniel and McKay are kidnapped by the new race and are forced to finish a device which may kill the Wraith. Todd feels betrayed and takes the Daedalus.

The new race that stole the device, not to mention Rodney and Daniel, turns out to be an old one meaning very old and well known to the human race. With an ancient grudge to settle, they force Rodney to activate the device against the Wraith with a side effect that could kill millions throughout the galaxy. That makes the Wraith mad so they abscond with the Daedalus to retaliate. Once again we lowly humans have to take control of a messy situation to keep the master races from wreaking havoc in the galaxy.

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 Wraith cruiser arrives at Atlantis and is strangely uncommunicative.

The killings of a Wraith in Las Vegas are investigated by Detective John Sheppard - who knows nothing about life-sucking aliens from another galaxy.

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.