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 "The Kindred Part 1"
- Written by: Joseph Mallozzi
- Directed by: Peter Woeste
- 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) "We needed the energy as we finally finished breaking Rise of the Googlions Part I today. I’ll be doing the honors, which means I get to work on the outline this weekend." (Joseph Mallozzi's June 8 blog) "Well, spent most of the early afternoon writing the outline for Rise of the Googlions Part I. A number of pieces fall into place as many of the things we’ve been building toward come to fruition (and not in a sweet apple sort of way either). Surprises in store; revelations galore." (Joseph Mallozzi's June 9 blog) "Back at work today and I’m pleased to report I completed the Tease of my newly retitled script - The Kindred, Part I." (Joseph Mallozzi's June 18 blog) "Oh, dear. How depressing. My three-week hiatus is almost over and what have I got to show for it? One script completed, less than 20 books read, and a peeling sunburn. [...] Paul, meanwhile, phoned me up to discuss some of the changes he wants to make to Kindred I. The fact that wraith ships don’t possess shields certainly complicates matters, but I’ve always loved Paul’s idea of giving them limited regenerative capabilities. And, if it survives the polish, we get to find out where Lorne grew up. Any guesses? We’ll be back in the offices on Monday [July 16] [and] it looks like a week of meetings for yours truly as we head directly into prep on Kindred I, to be directed by SG-1 alumni Peter Woeste." (Joseph Mallozzi's July 12 blog) "We watched the director’s cut of Spoils of War [...], then gave/got notes on The Kindred Pt. 1 (just a few page notes and a suggestion for a Caldwell scene), which took us to lunch. [...] The concept meeting was fabulous - as far as concept meetings go. First A.D. Bill Mizel was at his curmudgeony best, leading us through the narrative masterpiece, occasionally stopping to interject his misgivings about fire gags, background extras, and the confusing misuse of the term “CG wraith” which it turns out does NOT stand for Computer Generated." (Joseph Mallozzi's July 16 blog) "Also, congratulations to me for finally getting handle on that Caldwell-Sheppard Daedalus scene that will touch on the repercussions from an earlier episode. Now, all I have to do is write it." (Joseph Mallozzi's July 19 blog) In an audition for a role in this episode, one of the lines for a male character was, “Same as you. Scavenging the ruins of a dead world.” (Joseph Mallozzi's July 20 blog) "We also started shooting Kindred I today. Check out the pics." This episode appears to be one of the 14 for Carter. (Joseph Mallozzi's July 24 blog) "After a day of shooting Kindred I, we’re shooting the final day of Miller’s Crossing, then will be switching back to Kindred I when we return on Monday." (Joseph Mallozzi's July 25 blog) "Pete Woeste is shooting day two of Kindred I down on Stage 6. Scenes up today: team geared for mission, Sheppard’s update, Lorne delivers the news, parlay, and the situation room." Mallozzi also includes pictures taken on the set, including one with Paul McGillion. (Joseph Mallozzi's July 30 blog) "Day 3 of Kindred I took the cast and crew to Green Timbers, a location shoot that necessitated our ordering in. [...] Oh, and in dailies today = the wee turtles!" (Joseph Mallozzi's July 31 blog) We find out where Lorne is from in Kindred I. (Joseph Mallozzi's August 2 blog)
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4.xx "The Kindred Part 2"
- Written by: Alan McCullough
- 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) "Alan will be tackling Rise of the Googlions Part II which we’ll start spinning next week along with Martin’s next episode." (Joseph Mallozzi's June 8 blog) "Today, we gave Alan notes on his outline, discussed Midway, and had a very brief discussion of Martin’s next episode which we should start breaking tomorrow. That will leave three scripts to be written when we get back: the Joe F. story, Paul’s season finale idea, and the empty slot." (Joseph Mallozzi' June 18 blog) "Alan is plugging away on Kindred II which is an episode fans will no doubt be looking forward to. No pressure, Alan." (Joseph Mallozzi's July 12 blog) "Congratulations to Alan McCullough who handed in his first draft of Kindred II. There won’t be a dry eye in the house when this one airs." (Joseph Mallozzi's July 19 blog) "Paul and Alan are prepping Kindred II..." (Joseph Mallozzi's July 25 blog)
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4.xx "Midway"
- 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) "Carl has finished revising Quarantine and already has an outline in place for Midway." Most probably this refers to the Midway Space Station (we're currently assuming the title "Midway" applies to this particular episode). As far as which SG-1 characters will be present in the "big crossover", there are no plans to bring Ben Browder or Claudia Black into Season Four. (Joseph Mallozzi's June 8 blog) Concerning which SG-1 character will be crossing over, "Will let you know once his deal has been closed." (Joseph Mallozzi's June 18 blog) "Today, we gave Alan notes on his outline, discussed Midway, and had a very brief discussion of Martin’s next episode which we should start breaking tomorrow. That will leave three scripts to be written when we get back: the Joe F. story, Paul’s season finale idea, and the empty slot." (Joseph Mallozzi's June 18 blog) "After taking time off to do a little fishing, Carl is heavy into Midway. It’ll be great to finally see the big men spar. It’ll also be nice to have Kavanagh back. Unfortunately, he won’t find his return quite as enjoyable." (Joseph Mallozzi's July 12 blog) "Carl managed to put out his Final Draft of Midway (Final Draft being a misnomer really since he’ll be revising that sucker between now and about two days after it’s been shot)." (Joseph Mallozzi's July 25 blog)
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4.xx "Trio"
- Written by: Martin Gero
- 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) "Today, we gave Alan notes on his outline, discussed Midway, and had a very brief discussion of Martin’s next episode which we should start breaking tomorrow. That will leave three scripts to be written when we get back: the Joe F. story, Paul’s season finale idea, and the empty slot." (Joseph Mallozzi' June 18 blog) "Well, I’m pleased to report that we made some headway on Martin’s script, Foxy Loxy with Floppy Socksies (Think about it! All the clues you need are right in the title!), hashing out some of the major beats and act breaks in an episode that promises to be a lot of fun." (Joseph Mallozzi's June 21 blog) "Marty G. has taken his birthday festivities on the road - Vegas to be precise, where he reports he is 15 pages into his next script which still has no title, but does have Rodney driving Carter and Keller absolutely crazy." (Joseph Mallozzi's July 12 blog) "We spent the better part of the morning spinning Joe F.’s notion into the actual beginnings of a story. Due to a schedule sleight-of-hand, Marty G. will be taking a break from that troubled trio script to tackle this one." (Joseph Mallozzi's July 21 blog) "...Marty G. is finding out that his little Three’s Company episode aint gonna be as little as he thought." (Joseph Mallozzi's July 25 blog) "To all of you Sam fans dying for a hint of what’s going on with Carter’s love life, you’ll have to wait until Trio for a not-so-subtle tip-off." (Joseph Mallozzi's August 2 blog) "Martin was writing the Sheppard on Earth story but, having finished Trio (formerly Three’s Company), he will start on Harmony while Alan McCullough assumes writing duties on the JF-inspired eppy. [...] We will not be dealing with Sam’s love life on Atlantis. However, a passing mention of her personal life during a candid moment is another matter." (Joseph Mallozzi's August 3 blog)
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4.xx Flanigan's Earth-Based Episode
- Story by: Joe Flanigan
- Teleplay by: Alan McCullough
- 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) "Then comes Joe F.’s story, still in play, and Paul’s season finale. Send in the Clones is toast." (Joseph Mallozzi's June 8 blog) "Today, we gave Alan notes on his outline, discussed Midway, and had a very brief discussion of Martin’s next episode which we should start breaking tomorrow. That will leave three scripts to be written when we get back: the Joe F. story, Paul’s season finale idea, and the empty slot." (Joseph Mallozzi' June 18 blog) "No new details until Monday [July 23] when we’re scheduled to start breaking it." (Joseph Mallozzi's July 19 blog) "We spent the better part of the morning spinning Joe F.’s notion into the actual beginnings of a story. Due to a schedule sleight-of-hand, Marty G. will be taking a break from that troubled trio script to tackle this one. We discussed the basic premise, the type of story to tell, and also started hashing out some of the Sheppard backstory. What brings Sheppard back to Earth? Who goes with him? Which individuals from his past will put in an appearance? What’s at issue? How will the action progress? Although we didn’t get around to actually breaking the story, we’re all pretty happy with the direction we’ve taken." (Joseph Mallozzi's July 21 blog) "Finally, we will get around to breaking that Sheppard on Earth story next week along with what we hope will be the season finale." (Joseph Mallozzi's August 2 blog) "We started spinning the story but took a break to work on Harmony, then will switch gears again to work on the Sheppard on Earth story next week. Martin was writing the Sheppard on Earth story but, having finished Trio (formerly Three’s Company), he will start on Harmony while Alan McCullough assumes writing duties on the JF-inspired eppy." (Joseph Mallozzi's August 3 blog)
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4.xx "Harmony"
- Written by: Martin Gero
- Directed by:
- Storyline:
- Production Notes: "Today, we gave Alan notes on his outline, discussed Midway, and had a very brief discussion of Martin’s next episode which we should start breaking tomorrow. That will leave three scripts to be written when we get back: the Joe F. story, Paul’s season finale idea, and the empty slot." (Joseph Mallozzi' June 18 blog) "The last story slot has finally been filled. We spent most of yesterday spinning, then breaking Harmony which I am really, really, REALLY looking forward to. Alas, I won’t be writing it as Marty G. will be assuming said duties, but I have no doubt he’ll do a brilliant job AND have a lot of fun with it." (Joseph Mallozzi's August 2 blog) "Martin was writing the Sheppard on Earth story but, having finished Trio (formerly Three’s Company), he will start on Harmony while Alan McCullough assumes writing duties on the JF-inspired eppy." (Joseph Mallozzi's August 3 blog) "Harmony is not the season finale. The season finale has yet to be broken. Also, the production order of the episodes does not reflect their air order." (Joseph Mallozzi's August 5 blog)
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4.20 Finale
- Written by: Paul Mullie
- 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) "Today, we gave Alan notes on his outline, discussed Midway, and had a very brief discussion of Martin’s next episode which we should start breaking tomorrow. That will leave three scripts to be written when we get back: the Joe F. story, Paul’s season finale idea, and the empty slot." (Joseph Mallozzi' June 18 blog) "Finally, we will get around to breaking that Sheppard on Earth story next week along with what we hope will be the season finale." (Joseph Mallozzi's August 2 blog) "Harmony is not the season finale. The season finale has yet to be broken. Also, the production order of the episodes does not reflect their air order." (Joseph Mallozzi's August 5 blog)
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