4.01 "Adrift Part 2"
- With only 24 hours of life support remaining, the city-ship Atlantis is suspended somewhere in space without the use of the Stargate.
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4.02 "Lifeline Part 3"
- While the team risks going into the Replicators' city to obtain a ZPM to power the city-ship Atlantis, Col. Samantha Carter joins the crew of the Apollo to search for the missing base.
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4.03 "Reunion"
- Ronon is reunited with those from his homeworld and is asked to leave the Atlantis Expedition to rejoin them. Col. Samantha Carter becomes the new leader of the Atlantis Base.
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4.04 "Doppelganger"
- Sheppard encounters a psychopathic crystalline entity that takes on his likeness in his team's nightmares.
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4.05 "Travelers"
- Sheppard becomes the prisoner of a group of ship-faring people known as the Travelers who wish to use his Ancient gene to reactivate long-dormant Ancient technology — specifically, an Ancient Aurora-class battle ship.
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4.06 "Tabula Rasa"
- With almost everyone on Atlantis infected by an amnesia-causing bacteria, McKay finds himself zip-strapped to his desk with cryptic letters on his arm and no memories of who he is or what has happened.
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4.07 "Missing"
- Teyla's and Dr. Keller's friendly visit to New Athos turns into a matter of survival when they find the Athosians have disappeared and they are attacked by primitives.
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4.08 "The Seer"
- Atlantis encounters the Vedeenans and tries to save their ill leader, Davos. Davos appears to see the future, and predicts the destruction of Atlantis. Carter must decide how to react to his prophesy when the Wraith Todd proposes a collaboration but then brings the enemy to Atlantis.
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4.09 "Miller's Crossing"
- Jeanie McKay Miller and Dr. Rodney McKay are kidnapped by businessman Henry Wallace on Earth. Wallace wants the McKays to fix the nanites he implanted in his daughter to cure her cancer — they are malfunctioning. Wallace injects nanintes into Jeanie to make his point, and Rodney must rely on Todd and his team to save her.
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4.10 "This Mortal Coil Part 1"
- A rogue group of Replicators creates duplicates of Sheppard's team and Dr. Elizabeth Weir in the hope of discovering how to ascend like their creators, the Ancients.
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4.11 "Be All My Sins Remember'd Part 2"
- The Atlantis Expedition and the Wraith join forces to execute a daring plan against a common enemy.
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4.12 "Spoils Of War"
- The Atlantis team successfully salvage a partially damaged Hive ship and in the process retrieve some critical information that may help in their war against the Wraith.
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4.13 "Quarantine"
- Atlantis suddenly activates a quarantine lockdown, trapping personnel in various parts of the city with no way in or out and, more importantly, with no medical help.
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4.14 "Harmony"
- Always keen on helping their allies, Sheppard and McKay accept a proposal made by Harmony’s sisters to accompany her on a trek into the forest to seek guidance to become queen in her late mother’s stead. Will Harmony become the planet’s new queen, or will an enemy assassinate her — and her escorts?
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4.15 "Outcast"
- Sheppard returns to Earth for his father’s funeral and is enlisted to track down a human form Replicator created in an Earth lab.
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4.16 "Trio"
- On a diplomatic mission together, Carter, McKay and Keller fall into a subterranean mining facility left by the Genii. Every attempt to escape seems to put them in further jeopardy, and the constant tremors that shake their prison mean time is running out.
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4.17 "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.
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4.18 "The Kindred Part 1"
- A mysterious 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.
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4.19 "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.
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4.20 "The Last Man"
- Through a time anomaly, Sheppard winds up thousands of years in the future and finds the city almost completely buried in sand and a hologram of Dr. McKay, which lets him know how life changed after he went missing on a mission.
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