5.01 "Search And Rescue Part 2"
- A race against time pits Col. Carter's crew against Michael and his Wraith hybrids to recover the Atlantis team trapped in the rubble of Michael's facility.
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5.02 "The Seed"
- Dr. Carson Beckett is revived from the stasis chamber after an alien organism incapacitates Dr. Keller and triggers a quarantine of the Atlantis team.
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5.03 "Broken Ties"
- Ronon endures a grueling ordeal after his former friend, Tyre, captures and delivers him to the Wraith. Meanwhile, the team launches a rescue mission for their missing comrade.
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5.04 "The Daedalus Variations"
- A drive malfunction aboard a mysterious duplicate Daedalus sends the team jumping through various alternate realities where they encounter sinister alien life forms, a searing sun, and a pitched space battle over Atlantis.
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5.05 "Ghost In The Machine"
- Surviving human form Replicators wish to achieve ascension by uploading their consciousnesses into subspace to live indefinitely as fields of energy, but Atlantis is put into danger when their experiment yields some surprising results.
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5.06 "The Shrine"
- Dr. Rodney McKay faces death in the form of a fatal illness, leading to the depletion of his memories, behavioral regression and a trip to a special shrine.
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5.07 "Whispers"
- Sheppard and Beckett join Maj. Anne Teldy’s team on a planet with one of Michael’s research facilities for the early versions of his human-iratus hybrids concealed inside a cave system. Unfortunately, the explorers have a role in setting loose creatures that hunt down each of them as they get separated in a blinding fog.
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5.08 "The Queen"
- Teyla poses as Todd’s Queen to represent his hive in negotiations with an allied hive, but tension escalates as the alliance’s territories are threatened by another Wraith hive.
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5.09 "Tracker"
- Keller is abducted by the Runner Kiryk who brought the Wraith to a village on a planet where she, McKay, and Ronon were visiting. After helping the villagers to safety, McKay and Ronon set out to rescue Keller, running into booby traps left by the Runner along the way.
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5.10 "First Contact Part 1"
- Dr. Daniel Jackson comes to do research into the history of the Atlantian Ancient Janus who built a timeship in a puddle jumper 10,000 years ago. During his visit, a new enemy in the galaxy gets revealed.
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5.11 "The Lost Tribe Part 2"
- McKay and Daniel are caught in the middle of the war between the Wraith and another powerful race in the Pegasus Galaxy. Sheppard teams up with the Travelers to rescue the two after the Daedalus falls into enemy hands.
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5.12 "Outsiders"
- The Balarans are survivors of Michael’s release of the modified Hoffan drug and have joined the village of another planet as a place of refuge where Dr. Beckett is working in a clinic. They considered their survival as a blessing until they learn that the Wraith are on their way to their new homeworld to wipe them out.
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5.13 "Inquisition"
- The Atlantis Expedition is brought to trial by the Coalition for their “crimes against the people of the galaxy.”
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5.14 "The Prodigal"
- Michael uses his stolen puddle jumper to infiltrate Atlantis and take it over from the gate room. He is driven to take Teyla's son, and Teyla as well if she's willing. He intends to destroy Atlantis in vengeance for what was done to him. Sheppard and the Lanteans must stop Michael once and for all.
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5.15 "Remnants"
- Woolsey faces an uncertain future in the form of a performance evaluation; Zelenka and McKay examine an object discovered on the ocean floor; Sheppard encounters an ambush.
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5.16 "Brain Storm"
- McKay brings Keller to Earth to visit an old rival physicist at his secret research facility. The rival demonstrates a wonderful new invention that’s intended to fight global warming, but things do not go as planned.
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5.17 "Infection"
- A distress call from a hive ship over Atlantis leads the team to discover a Wraith crew in stasis, with all hands stricken with a disease caused in part by Dr. Keller's gene therapy.
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5.18 "Identity"
- An Ancient device on another planet causes Dr. Keller to swap bodies with a woman named Neeva, who hides her true identity from the Atlantis expedition. Once they realize what has happened, Sheppard’s team, with Dr. Carson Beckett along, must find and deactivate the device that caused the body swap. They must rescue Keller from people who believe she is Neeva, and who have troubles of their own.
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5.19 "Vegas"
- Detective John Sheppard investigates murders in Las Vegas linked to an unusual man with superhuman abilities.
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5.20 "Enemy At The Gate"
- Todd warns Atlantis about a sophisticated hive ship and encourages the team to attack the vessel before it can pose a threat to Earth.
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