The story of Stargate Atlantis follows the cliffhanger episode on Stargate SG-1's seventh season finale "Lost City", where SG-1 found an outpost made by the race known as the Ancients in Antarctica. After the events of Stargate SG-1 season eight premiere "New Order", the Stargate Command sends an international team to investigate the outpost. Soon, Dr. Daniel Jackson discovers the location of the greatest city created by the Ancients, Atlantis. The story unfolds when the members of the expedition encounters the Wraith, the race that defeated the Ancients ten thousand years ago.
Stargate Atlantis - S02E01 - The Siege: Part 3(Aired: 19 July 2006) 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.
Stargate Atlantis - S02E02 - The Intruder(Aired: 26 July 2006) 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.
Stargate Atlantis - S02E03 - Runner(Aired: 2 August 2006) 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.
Stargate Atlantis - S02E04 - Duet(Aired: 9 August 2006) After an attempt to retrieve McKay and LT Laura Cadman from the memory banks of a Wraith dart, Cadman gets stuck in McKay's mind.
Stargate Atlantis - S02E05 - Condemned(Aired: 16 August 2006) The team discovers a planet where the stargate is kept on a prison island to keep the Wraith satisfied. Their magistrate is willing to trade a rare mineral.
Stargate Atlantis - S02E06 - Trinity(Aired: 23 August 2006) The team discover an Ancient project to create the ultimate power source. McKay thinks he can finish it. Ronon finds out he is not the only surviving Satedan.
Stargate Atlantis - S02E07 - Instinct(Aired: 30 August 2006) The team find a hidden Wraith girl, cared for by a man with a serum stilling her hunger. Beckett wants to perfect a retrovirus turning Wraith into Humans.
Stargate Atlantis - S02E08 - Conversion(Aired: 6 September 2006) Sheppard is infected with the Wraith retrovirus and slowly turns into an Iratus bug. To provide a treatment stem cells must be retrieved from one of their eggs.
Stargate Atlantis - S02E09 - Aurora(Aired: 13 September 2006) McKay finds an Ancient warship adrift in space. Sheppard finds out they are carrying a communique that mentions a weakness in Wraith technology.
Stargate Atlantis - S02E11 - The Hive(Aired: 27 September 2006) Sheppard's interrogation is suddenly aborted. Teyla senses another hive ship has arrived. Meanwhile McKay tries to convince his guard to call in help.
Stargate Atlantis - S02E12 - Epiphany(Aired: 4 October 2006) The teams discovers a ridge that can only be entered through a door. Sheppard gets pulled in by a field. McKay discovers time goes very fast behind it.
Stargate Atlantis - S02E17 - Coup D'etat(Aired: 15 November 2006) While Teyla and Ronon investigate the mysterious death of major Lorne, the Genii Ladon Radim contacts Atlantis. He wants to trade in a ZPM.
Stargate Atlantis - S02E18 - Michael(Aired: 22 November 2006) Michael Kenmore, a new lieutenant, awakes in the infirmary and doesn't remember a thing. The crew is very concerned about his well-being, he seems different.
Stargate Atlantis - S02E19 - Inferno(Aired: 29 November 2006) Atlantis helps with repairing an Ancient shield generator on Taranis. They discover the Taranians are in possession of an Ancient warship.
Stargate Atlantis - S02E20 - Allies(Aired: 6 December 2006) The hive ship approaching Atlantis is Michael's. He wants a trade: the retrovirus for not revealing the secret of Atlantis and insights on Wraith technology.