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"
- 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.xx Flanigan's Earth-Based Episode
- Story by: Joe Flanigan
- Teleplay by:
- Directed by:
- Storyline:
- Production Notes: "We start the spinning. There’s the other Earth-based episode Joe F. pitched out. The return-of-that-character two-parter with its Fargo-esque first part, the big team-up eppy, and the puzzle piece." (Joseph Mallozzi's June 1 blog)
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4.xx Second-Half-Season Two-Parter - Part 1
- Written by: Carl Binder
- Directed by:
- Storyline:
- Production Notes: "I am pleased to announce that Carson Beckett will be returning to Atlantis for a two-part story in the back half of season four. When he returns for the two-parter, it will be Carson Beckett in the flesh. Late in season three, we discussed the manner in which the character had been written out and the possible ways in which he could be brought back. I threw out an idea that not only brought Carson back, but answered a very big question I had concerning a late-season arc. In order to lay the groundwork for his possible return, we threaded a subtle hint into one of the late season three episodes. So, if fans want to know how we plan on bringing the good doctor back from the dead, they should seek out the hidden clue when the back half of season three returns to SciFi this Friday, April 13th. Well, I don’t want to give too much away but I can say it won’t be an AU version of Carson - or a time-hopping Dr. Beckett either." (Joseph Mallozzi in an interview at the Save Carson Beckett Campaign Site, April 9, 2007) "Then there’s the two-part return of THAT character. Which brings us to episodes 17." (Joseph Mallozzi's May 7 blog) "Alas, the Beckett episode count is presently at 2 because the planned third episode was temporarily shelved." (Joseph Mallozzi's May 10 blog) "We start the spinning. [..] The return-of-that-character two-parter with its Fargo-esque first part..." (Joseph Mallozzi's June 1 blog) "After all lunch, we finally started work on the first part of the late season two-parter, what Carl has tentatively titled “Rise of the Googlions”." (Joseph Mallozzi's June 6 blog)
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4.xx Second-Half-Season Two-Parter - Part 2
- Written by:
- Directed by:
- Storyline:
- Production Notes: "I am pleased to announce that Carson Beckett will be returning to Atlantis for a two-part story in the back half of season four. When he returns for the two-parter, it will be Carson Beckett in the flesh. Late in season three, we discussed the manner in which the character had been written out and the possible ways in which he could be brought back. I threw out an idea that not only brought Carson back, but answered a very big question I had concerning a late-season arc. In order to lay the groundwork for his possible return, we threaded a subtle hint into one of the late season three episodes. So, if fans want to know how we plan on bringing the good doctor back from the dead, they should seek out the hidden clue when the back half of season three returns to SciFi this Friday, April 13th. Well, I don’t want to give too much away but I can say it won’t be an AU version of Carson - or a time-hopping Dr. Beckett either." (Joseph Mallozzi in an interview at the Save Carson Beckett Campaign Site, April 9, 2007) "Then there’s the two-part return of THAT character. Which brings us to episodes 17." (Joseph Mallozzi's May 7 blog) "Alas, the Beckett episode count is presently at 2 because the planned third episode was temporarily shelved." (Joseph Mallozzi's May 10 blog) "We start the spinning. [...] The return-of-that-character two-parter with its Fargo-esque first part..." (Joseph Mallozzi's June 1 blog)
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4.xx Big Crossover Episode
- Written by: Carl Binder
- Directed by:
- Storyline:
- Production Notes: There will be an SG-1 crossover episode, but when asked if Michael Shanks as Daniel Jackson will be included, Mallozzi responded, "It’s possible but we have another actor in mind for the big crossover episode that Carl will be writing." (Joseph Mallozzi's April 15 blog) "And Carl has started work on the relationships episode. He’ll be moving onto the cross-over episode once he’s done." (Joseph Mallozzi's May 7 blog) "We start the spinning. There’s the other Earth-based episode Joe F. pitched out. The return-of-that-character two-parter with its Fargo-esque first part, the big team-up eppy, and the puzzle piece." (Joseph Mallozzi's June 1 blog)
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4.xx Puzzle Piece Episode
- Written by:
- Directed by:
- Storyline:
- Production Notes: "We start the spinning. There’s the other Earth-based episode Joe F. pitched out. The return-of-that-character two-parter with its Fargo-esque first part, the big team-up eppy, and the puzzle piece." (Joseph Mallozzi's June 1 blog)
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4.19 Penultimate Episode
- Written by:
- Directed by:
- Storyline:
- Production Notes: The last two episodes of the season "will not be a two-parter." (Joseph Mallozzi's June 6 blog)
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4.20 Finale
- Written by:
- Directed by:
- Storyline:
- Production Notes: "We also took the time to discuss [...] Paul’s very cool idea for the season (?) finale, a little episode we’re calling…“Finale“. The last two episodes of the season "will not be a two-parter." (Joseph Mallozzi's June 6 blog)
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