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.

Rodney investigates a ZPM from a planet whose inhabitants kill themselves when they turned 25 years old to prevent the Wraith from feeding on them.

Atlantis offers help to the Hoffans, who are working on a defense against the Wraith.

Atlantis wants to trade food with the Genii, a simple civilization who turn out to be not so simple. They are planning a nuclear attack against the Wraith.

A strange energy generating fog allows travel back to Earth. But something's wrong.

Two hurricanes are approaching Atlantis and an evacuation is necessary. The leader of the planet taking them in tells the Genii about the situation.

McKay and Weir start repairing the grounding station, while Sheppard tries to fight Kolya. The puddle jumper on the mainland enters the eye of the storm.

Major John Sheppard, Rodney McKay and two scientists explore a planet where a Wraith spaceship, which crashed there 10,000 years ago, during the Atlantis-Wraith War, is still sending a SOS signal.

A team of scientists, including McKay, Zelenka and Ford, are exposed to a deadly virus. Sheppard goes after one of the scientists trying to escape.

Sheppard invites a priestess, who claims to not know about a weapon protecting her planet from the Wraith, to Atlantis to discuss asylum for refugees.

It's Elizabeth's birthday and she gets a very special gift: a woman who has been in stasis in an Atlantis' laboratory for 10,000 years and is actually herself.

The team is on Dagan, where they must find key stones to retrieve a ZPM. Zelenka finds out Atlantis has a deep space scanner.

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.

Teyla is haunted by nightmares, leaving her agitated. After seeing a psychologist, an old Athosian woman tells her a secret about her ability to sense the Wraith.

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.

All hope seems lost, until Colonel Everett arrives suddenly from Earth. He is determined to defend the city until the arrival of a ZPM, brought by a new ship.

The Daedalus arrives and the two hive ships are destroyed. Atlantis seems saved, then Zelenka detects 12 more ships. Ford seems changed after a fall in the water.

McKay, Sheppard, Beckett and Weir are on the Daedalus. McKay finds a Wraith virus that is infecting ship systems and sending a signal to the Wraith.

The team is searching for Ford on a planet. Teyla and Sheppard are taken hostage by a stranger, while Ford tries to convince McKay that he's normal.

The team is captured by Ford and are forced to take the Wraith enzyme. Ford has a plan.

Sheppard's interrogation is suddenly aborted. Teyla senses another hive ship has arrived. Meanwhile McKay tries to convince his guard to call in help.

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.

The team is captured by Ford and are forced to take the Wraith enzyme. Ford has a plan.

Teyla is haunted by nightmares, leaving her agitated. After seeing a psychologist, an old Athosian woman tells her a secret about her ability to sense the Wraith.

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

Sheppard's interrogation is suddenly aborted. Teyla senses another hive ship has arrived. Meanwhile McKay tries to convince his guard to call in help.

The Daedalus arrives and the two hive ships are destroyed. Atlantis seems saved, then Zelenka detects 12 more ships. Ford seems changed after a fall in the water.

Major John Sheppard, Rodney McKay and two scientists explore a planet where a Wraith spaceship, which crashed there 10,000 years ago, during the Atlantis-Wraith War, is still sending a SOS signal.

The team is searching for Ford on a planet. Teyla and Sheppard are taken hostage by a stranger, while Ford tries to convince McKay that he's normal.

Rodney investigates a ZPM from a planet whose inhabitants kill themselves when they turned 25 years old to prevent the Wraith from feeding on them.

Atlantis offers help to the Hoffans, who are working on a defense against the Wraith.

A strange energy generating fog allows travel back to Earth. But something's wrong.