Adrift Dr. Weir clings to life and Dr. McKay tries to save Atlantis, which is badly damaged and lost in space after the Replicator attack.
Lifeline McKay and Sheppard prepare to steal a ZPM from the Replicator home world; Colonel Samantha Carter links up with the Apollo to search for Atlantis.
Reunion A mission against the Wraith has the Atlantis team collaborating with a group of Satedans from Ronon's past.
Doppelganger While exploring a jungle planet, Lt. Colonel Sheppard comes into contact with a crystalline growth that turns him into a host for an infectious alien life form.
Travelers On a return flight to Atlantis, a jumper is seized and its pilot, Lt. Colonel Sheppard, is taken prisoner by Larrin, the commander of a rogue human ship.
Tabula Rasa The crew suffers from amnesia after plant samples from their new home planet unleash a virus that affects everyone except Teyla and Ronon.
Missing Teyla and Dr. Keller uncover a mystery on New Athos, where they find an abandoned Athosian settlement and a hostile warrior tribe.
The Seer Atlantis receives a visitor with psychic abilities, who delivers a dark forecast about the outpost.
Miller's Crossing Jeanie Miller, Dr. Rodney McKay's sister, is kidnapped on Earth, prompting a response from the Atlantis team.
This Mortal Coil A strange drone crashes into Atlantis, heralding a dreadful new predicament.
Be All My Sins Remember'd The team takes on Replicators in a two-pronged attack as the Apollo and the Daedalus face an armada, while McKay works with a Wraith scientist to thwart their common foe. Further complicating things, Larrin resurfaces.
Spoils Of War The Atlantis team salvages a damaged Wraith vessel, which turns out to hold valuable tactical information about the group's enemies.
Quarantine A quarantine begets a lockdown on Atlantis, trapping Rodney in the botany lab with Katie Brown.
Harmony Sheppard and McKay become escorts on a young princess's rite of passage and run afoul of the would-be queen's enemies.
Outcast Sheppard learns that his father has died and returns to Earth for the funeral, accompanied by Ronon. While there, they discover that a covert project has accidentally unleashed a human-form Replicator in the city.
Trio A subterranean drama unfolds when Col. Carter and Doctors McKay and Keller become trapped in a defunct mining facility during an off-world mission.
Midway Teal'c goes to Atlantis to mentor Ronon ahead of an IOA review to determine his suitability for the Stargate program. Meanwhile, the Wraith kick-start a plot against the Midway station.
The Kindred, Part 1 A mystery illness wreaks havoc on humans across the Pegasus galaxy; Teyla's vision about the father of her child prompts her to join Sheppard on a mission that yields an unexpected discovery.
The Kindred, Part 2 Beckett's return surprises the Atlantis crew. Elsewhere, Teyla, now a prisoner, finds missing Athosians held captive at one of Michael's secret facilities.
The Last Man Sheppard returning to a derelict Atlantis amid a sea of sand dunes thousands of years after his last search for Teyla, but a hologram of an aged Dr. McKay has a plan to set things right.