3.01 "No Man's Land Part 2"
- Sheppard's ship vanishes during a space melee against the Wraith. Meanwhile, Weir is recalled to Stargate Command as Col. Caldwell leads a mission to keep the Wraith from reaching Earth.
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3.02 "Misbegotten Part 3"
- Richard Woolsey travels to Atlantis to evaluate Dr. Weir's leadership. Meanwhile, Dr. Beckett and Sheppard are at odds over what to do with the former Wraith transformed into humans by the retrovirus.
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3.03 "Irresistible"
- The team searches for Stargates to harvest for an intergalactic bridge, and encounters a charming alchemist who beguiles Dr. Beckett.
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3.04 "Sateda"
- While on an exploratory mission, Ronon is taken prisoner by villagers who made a pact with the Wraith. Meanwhile, Sheppard and Teyla rally the team to rescue their comrade.
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3.05 "Progeny"
- An advanced civilization is accidentally discovered during the team's investigation of a purportedly abandoned Ancient testing site, prompting Weir to broker an alliance with the society's leader, Oberoth.
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3.06 "The Real World"
- Dr. Weir has a rude awakening in a psychiatric hospital on Earth, where she is told that her memories of Atlantis are delusions.
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3.07 "Common Ground"
- An ambush leaves Col. Sheppard a prisoner of the Genii. While Dr. Weir tries to figure out who Atlantis's allies and enemies really are, Sheppard must risk an unlikely alliance to gain his freedom.
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3.08 "McKay And Mrs. Miller"
- An experiment for drawing power from other dimensions draws the attention of an alternate universe's Dr. Rodney McKay, who says the research will destroy his universe. Unfortunately, the second McKay's plan to save his universe will destroy this one.
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3.09 "Phantoms"
- The Atlantis team is stranded on a mysterious planet, where the effects of an abandoned Wraith experiment threaten to turn them against one another.
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3.10 "The Return Part 1"
- The Ancients, long believed to be extinct, return in force to Atlantis and reclaim the city for themselves — expelling Weir's team back to Earth.
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3.11 "The Return Part 2"
- Sheppard and his reunited team return to Atlantis to save the city from the Asurans.
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3.12 "Echoes"
- The whales of Lantia congregate around the city and their whalesong creates serious side effects on the Expedition members. Are they there to communicate or to destroy?
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3.13 "Irresponsible"
- The team meets up again with Lucius and finds that he’s engineered an attack on a village, only to find that things have not entirely gone as planned.
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3.14 "Tao Of Rodney"
- McKay's mind is astonishingly evolved by technology meant to aid Ancients to achieve ascension. As his mental powers increase, so does his risk of death.
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3.15 "The Game"
- McKay and Sheppard participate in a SIMS-like game simulation which turns out to be very real and with very destructive effects.
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3.16 "The Ark"
- The team boards a crippled space station to discover people have been preserved there with the hope to outlive their enemy, the Wraith.
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