The Siege, Part 3 Colonel Caldwell reinforces the beleaguered Atlantis team as the Wraith mass for another assault. Meanwhile, a seriously wounded Lt. Ford's abnormally rapid recovery causes further worry as his behavior turns erratic.
The Intruder McKay discovers that a sinister artificial intelligence has infected the computers of the Daedalus after circuitry malfunctions result in the death of two scientists.
Runner The team's discovery of a Wraith's mutilated remains during an expedition leads to an encounter with local warrior Ronon Dex, who has information about the missing Ford.
Duet A new security officer is trapped inside McKay's body with its unwilling host after Dr. Zalenka botches the pair's transportation from a Wraith vessel. Also, Sheppard petitions Weir to allow Ronon to join the Atlantis team.
Condemned The team's suspicions are aroused when they arrive on the technologically advanced world of Olesia, where the population appears to be immune from the ravages of the Wraith. McKay and Sheppard soon discover why when their puddle jumper crash-lands on a secluded island.
Trinity McKay tries to harness an energy source hidden within a monolith constructed by the Ancients on a planet previously believed to have been destroyed by the Wraith. But his obsession with tapping the structure's power has deadly consequences.
Instinct A synthetic virus created by Dr. Beckett to revert Wraiths to human form puts Sheppard's life in jeopardy after the team encounters a girl in the early stages of Wraith development.
Conversion Beckett and McKay race to curb Sheppard's disturbing metamorphosis when he begins to exhibit Wraith traits after being exposed to a strange virus.
Aurora The Atlantis team crosses paths with the Aurora, a massive vessel ferrying a surprise set of passengers - Ancients.
The Lost Boys Sheppard and his team catch up with the erratic Lt. Ford, who enlists their help for his attack on a Wraith hive ship - a plan Sheppard equates with suicide. Unfortunately, the effects of the Wraith enzyme have made Ford immune to reason.
The Hive Dr. McKay injects himself with the Wraith enzyme in a scheme to rescue Sheppard, Teyla, Ronon and Ford from the Wraith hive ship, where they are being held hostage.
Epiphany The team discovers a portal on a distant planet that pulls Sheppard to another world, where he encounters a dangerous creature. Elsewhere, McKay learns troubling news about the portal.
Critical Mass Atlantis is threatened by a bomb planted by the Goa'uld. Meanwhile, two Wraith cruisers are on course for the ancient city and a saboteur is unmasked.
Grace Under Pressure A puddle-jumper test flight results in an ocean crash that leaves McKay trapped in a sinking ship.
The Tower The team meets a village leader on a distant planet who has the ability to protect his people from Wraith attacks.
The Long Goodbye The team discovers two pods orbiting a moon, and Sheppard and Weir are pitted against one another when the occupants of the pods seize control of their minds.
Coup d'Etat While investigating a fire in a village on a far-off planet, the team discovers that a major carrying the Ancient gene has disappeared, and a Genii coup may be at hand.
Michael Besieged by amnesia and nightmares in which he is a Wraith, Lt. Michael Kenmore learns there is more afoot on Atlantis than his recovery from a Wraith attack.
Inferno Weir persuades the leader of a village on a distant planet to evacuate his people to Atlantis when an investigation of tremors uncovers a supervolcano that's due for an eruption.
Allies The Wraith forges a truce with the team. Michael, the Wraith they tried to turn into a human, returns and seeks McKay's retrovirus to be used against rival factions in the Wraith civil war.