After coming across a crystalline species similar to one that Colonel Jack O'Neill encountered ten years ago, Lt. Colonel John Sheppard inadvertently carries its entity back to Atlantis. As it moves into other members, it's bent on destroying them in nightmares in the form of Sheppard, increasing in severity for each case.
Lt. Colonel John Sheppard's team explores the planet designated M3X-387, a jungle planet where it is night. They investigate a strange energy reading in the hopes of finding Ancient technology. However, they don't find anything, which makes Sheppard wanting to turn back. However, Dr. Rodney McKay will not let it go, since he had a bet with Dr. Radek Zelenka and he'd win if they didn't find anything. However, Sheppard became more frustrated and ordered everyone back. However, just as they do, McKay notices a strange crystal glowing all by its self out of a tree. However, when he is close enough, Sheppard compelled himself to touch it, which causes a massive shock which throws him about ten feet backwards. He claims he has no idea why he did that, but the crystal is now dead. They all return with the hopes of bringing in a science team to research further.
Back in Atlantis, Sheppard is checked on by Dr. Jennifer Keller, who can't find anything wrong with him, but tells him to no longer touch any "strange things", with which Sheppard easily complies. He leaves the infirmary with Teyla Emmagan and tells her to get some sleep, since it is late. While doing this, he pats Teyla on the back, which triggers a transfer of blue energy that neither person notices. They wish each other a good night.
Teyla sleeps and has a mysterious dream in which she is having dinner with Sheppard, with fine Athosian dishes. Ronon Dex states that they were "hooking up", then McKay is heard reciting a quote from the mission concerning the energy reading. Later, Sheppard tells her that nobody trusts her but him, since the ordeal with a Wraith Queen a few months ago. She then hears Wraith Darts and hears her father's voice. She tries to save him, only to see Sheppard, who is now a Wraith feeding on her. Teyla awakens from the nightmare, and looks very disturbed.
The next morning, she talks with the team about the nightmare, and that Sheppard was the "big, bad monster". Though this was only a dream, she leaves without finishing breakfast, with Sheppard believing that she is mad with him, and claims that he can't control people's dreams. Teyla speaks with Dr. Kate Heightmeyer concerning the dream and says she believes the way she feels for Sheppard as being related to it. She also says that she had several nightmares of Wraith attacks, but none as terrifying and realistic as the one she witnessed, meaning she is actually afraid of going to sleep again. After the session, Teyla goes to Keller to receive sleeping pills, so she can have a good nights sleep.
That night, Keller wakes up to an urgent radio call. She rushes to the infirmary, where she discovers Teyla with severe abdominal pain. Sheppard tells her that Teyla was getting a late night snack when she toppled over from the pain. From there, Keller notices a moving lump in her stomach. She desperately tries to help her, but is completely helpless when blood sprays all over the medics, and an alien insect is seen bursting from Teyla's stomach, killing her, with Sheppard thinking that this is very cool. However, that was also a dream.
Due to the realistic nature of the nightmare, she goes to the infirmary to get some sleeping pills, when Ronon and Sheppard suddenly appear, scaring her. They had been sparring through the night, and Sheppard got in a lucky shot cutting Ronon's forehead. Ronon tells Sheppard to leave, so that Keller can stitch his cut, and have a rematch tomorrow. Keller tells Ronon to lie down, so she could treat him.
When she is done, Ronon walks out, heading for the Gate Room. However, he notices that no one is in and the city is completely abandoned. This somehow puts Ronon in a state of panic and frantically runs to find someone, until he opens a door, leading him to a forest. Now he is in a forest, when Wraith stun blasts blaze at him. He runs through the forest, dodging each shot. He is then knocked over, when Sheppard shows himself, and knocks him out with a stick. When Ronon regains consciousness, he is tied and bound in a pit, seeing Sheppard shoveling earth into it. Ronon tries to escape, but is ultimately buried alive. However, this was also just a dream, as Ronon slept through the stitches.
The next morning, Keller and the team begin to discuss their nightmares and notice that Sheppard seems to be involved in all of them, as a significant negative presence and that the nightmares occurred in a sequential pattern, from Teyla to Keller and then to Ronon. However, Ronon believes that the dreams were just coincidental random occurrences and doesn't give them a second thought. Keller, still concerned, approaches Colonel Samantha Carter about the problem and believes that it might have something to do with the crystal Sheppard touched back on M3X-387. However, their conversation is cut short when there is a situation in Crew quarters atrium.
In the atrium, a dazed and tired Major Evan Lorne holds Sheppard at gunpoint, where he accuses him of being a Replicator. The surrounding armed team and Heightmeyer attempts to talk him into lowering the gun, but Lorne refuses to do so, until someone either brings in an Anti-Replicator gun, or shoot Sheppard to prove his point. Carter approaches and calls for the ARG, which might help Lorne lower his gun. However, Lorne then accuses her of being a Replicator. He is actually about to fire his weapon, when Ronon saves them both and stuns him.
Lorne later wakes up, and tells them that he did not know what happened, and that he was glad no one was actually hurt. He theorizes that he was sleepwalking because of the lack of sleep, but didn't have an incident like that since he was ten years old. The Atlantis team realizes that a serious problem is brewing and decide to lock down the city and perform no off-world missions and gate travel is only as-needed. During a meeting, it is theorized that the crystal Sheppard touched contained an alien entity that feeds off people's fears, and may even take sadistic pleasure in harming its hosts. After some discussion, they decide to go back to M3X-387 to gather the crystal Sheppard touched, despite McKay's protests.
The team returns to the planet on which they found the crystal and manage to find a second one, which is active as well as the original. They bring both crystals back to one of the labs for further study. McKay and Zelenka theorize that the crystals need conductive material for transport, so they confine them in glass containers. Keller feels the impulse to touch one, but is fortunately stopped by Zelenka. With their new data, McKay and Zelenka scan Lorne to try and find the entity, but don't detect it. They then realize that the crystal entity is transporting itself via the city's power conduits, which means it can be anywhere. During more bickering, Keller again feels compelled to touch the live crystal, until she is stopped. She swears she has no idea why she did that, when McKay tells her that this is the way they "rope in its victims".
Meanwhile, outside, Teyla sees Heightmeyer standing on the edge of a railing, proclaiming that she doesn't want to die, but still can't walk to safety. She pleads for Teyla's help. However, Sheppard suddenly appears and prevents her from doing so. Teyla can only watch as Heightmeyer topples off the railings and falls down to the water below. The sequence is revealed to be another nightmare. Keller is summoned to Heightmeyer's quarters by Teyla, who tried to wake her up after she didn't report for duty, but couldn't. Keller finds Kate in her bed, dead. Faced with this threat, Carter is forced to put the city into full lockdown, where Keller tells her that she said the right words, despite the circumstance. Sheppard tried to come to Teyla, only to see her coming to him instead.
Fortunately though, Zelenka finally manages to create a program that can track the alien entity, but discovers that McKay is now infected. He sends McKay over to the room where he notices the rubber walls. After Zelenka leaves, McKay realizes that he is now infected. The rest of the team try to figure out a way to eradicate the alien entity. Sheppard comes up with a plan that if he could somehow contact McKay in his dreams, he can help him communicate with the alien entity and hopefully make it leave. Carter is then suddenly struck with an idea, and uses the equipment from the virtual reality pods SG-1 encountered on a mission in 1998 that can link people's minds in a virtual environment.
The team prepares to hook Sheppard into the machine. McKay thanks him in advance for trying. Soon, McKay sleeps, and has a dream that he is rowing a boat in the middle of the ocean, with Atlantis in the distance. It is heavily raining. He then notices a whale coming up to him. Sheppard then appears, but this one tells him to give up. The real Sheppard then shows up, and helps McKay row back to the city, telling the nightmare-Sheppard that he can't hurt him. However, nightmare-Sheppard tells them that they're wrong and summons the whale, which jumps up and swallows the boat and all of its occupants.
Sheppard wakes up to find the medical team trying to resuscitate McKay, but with no success. Keller apologizes and confirms that McKay is dead. Sheppard leaves the room, distraught over the death of Rodney. As he is trying to come to terms with events, the rest of the team arrive and begin to blame Sheppard for McKay's death. It is at that moment however, that Sheppard looks up and sees himself watching from the other side of the hall, he realizes that he is still dreaming and tackles the enemy through a wall and into the gate room.
Meanwhile, in the real world, Keller manages to resuscitate McKay and save his life, but Sheppard hasn't awakened yet, since the entity is now inside him. They notice his vitals spike, and can't revive him without risks of serious trauma or even death. However, McKay has an idea, and tells Keller to hook him up to the VR again. Back in the dream, Sheppard begins to fight with the alien entity in hand-to-hand combat inside the gate room, but nightmare-Sheppard quickly gains the upper hand. The real Sheppard gets thrown around and seriously beaten by his evil counterpart. Afterwards, nightmare-Sheppard urges him to fight. However Sheppard declines, telling him that is what he wants. There, McKay appears and confronts nightmare-Sheppard, telling him his vulnerable to electric shock, which is why he didn't kill McKay. In the real world, Keller begins using a defibrillator on Sheppard. Because the alien entity is composed of electrical signals, the electric shock from the defibrillator weakens it. Sheppard takes advantage of the opportunity and throws the alien entity through the Stargate.
Sheppard and McKay both wake up in the isolation room, and the crystal is glowing again, signaling that the alien entity is back inside. The team returns the two crystals back to their home planet, when the entire jungle begins to light up with countless crystals. The team beats a hasty retreat back to Atlantis, where none of them seem to be able to get any sleep and all meet in the mess hall in the middle of the night.
Sheppard: Looks like one of those toys you play with when you're a kid.
McKay: A Commodore 64?
Ronon: Triple-barrel shotgun?
Sheppard: A kaleidoscope.
(McKay talks about his past nightmares)
Sheppard: I can't control what's in her dreams.
McKay: Really, you think you can't control a person's dreams. My father read me Moby Dick when I was seven years old. I mean seriously, what was the man thinking? Do you have any idea how long I had nightmares about being eaten by a whale?
Ronon: They haven't stopped, have they?
(Discussing the movie Alien after Teyla, Dr. Keller, and Ronon's dreams)
McKay: So, very tense, working like a charm, Jocelyn's all freaked out beside me, I'm packing away the goobers and popcorn...and then the alien bursts out of John Hurt...
Teyla: You didn't.
McKay: Mm hm. Puked, all over her.
Ronon: I've got to see this movie.
Keller: Have you had any nightmares recently?
McKay: Not a night goes by. Last night, I dreamnt, that um Colonel Carter invited me to her quarters for dinner.
Teyla: Maybe you shouldn't be telling us this Rodney.
Keller: Yeah, I said nightmare, not delusional male fantasy.
McKay: Wait and listen. Turns out she was serving lemon chicken. I mean lemon. And the only reason she invited me to dinner was to tell me she was promoting Zelenka over me.
Ronon: That's it?
McKay: Then I was eaten by a whale. Don't ask how that happened.
(A sleepwalking Lorne demands Sheppard and Carter be shot with an ARG before being stunned)
Teyla: (holding the ARG) I take that I don't have to shoot either of you with this?
Sheppard: Yeah, you know, help him out; give him a little moral support. Come on -- all the things you've seen, you've never come across a way for one person to get into another person's dreams?
(Sam is way ahead of him and has been having a lightbulb moment for the past few seconds. Without saying anything, she heads out to the Control Room.)
Dex: Where's she going? What's going on?
Sheppard: I don't know, but I think I'm about to see a side of McKay I never wanted to see.
Mckay: You sure about this?
Sheppard: Not really.
(Rodney gestures to his own head, looking both plaintive and apologetic.)
Mckay: I'm pretty screwed up.
Sheppard: You're tellin' me!
(In McKay's dream, where both Sheppard and McKay row in the pouring rain)
Sheppard: You know, this isn't really as strange as you led me to believe.
McKay: Oh, yeah. What about that? (Points to the clown behind them)
Sheppard: I hate clowns!
(In Sheppards dream after defeating evil Sheppard.)
McKay: Okay this is really weird.
Sheppard: You're telling me
McKay: I thought there'd be more... you know hot girls.
- Joe Flanigan as Lt. Colonel John Sheppard/Crystal of M3X-387
- Amanda Tapping as Colonel Samantha Carter
- Rachel Luttrell as Teyla Emmagan
- Jason Momoa as Ronon Dex
- David Hewlett as Dr. Rodney McKay
- Jewel Staite as Dr. Jennifer Keller
- Claire Rankin as Dr. Kate Heightmeyer
- David Nykl as Dr. Radek Zelenka
- Kavan Smith as Major Evan Lorne
- Linda Ko as Marie
- Yee Jee Tso as Technician
- Tiffani Timms as Ellen (Uncredited)
- Ari Solomon as Billick (Uncredited)
- Tony Baretta as Smitty (Uncredited)
- Eddy Huber as Coughlin (Uncredited)
- Craig Fraser as Marine (Uncredited)
- D. Harlan Cutshall as Marine (Uncredited)
- ? as Marine
- When Dr. Rodney McKay asks "Do you know how many gate addresses in the ancient database have no accompanying description?" Lt. Colonel John Sheppard replies "Forty two?", a reference to The Hitchhiker's Guide to the Galaxy.
- The episode makes an allusion to Star Trek, when Sheppard wonders whether his evil self had a goatee. This parallels the Mirror universe, since the Mirror Universe double of Mr. Spock has a goatee.
- This episode was nicknamed "Nightmare on Atlantis Street" around the show's production office since the Crystal of M3X-387 enters dreams like Freddy Kruger in Nightmare on Elm Street.
- The scene in which Dr. Jennifer Keller sees the Iratus bug burst out of Teyla Emmagan's stomach is an allusion to the chestburster scene from Alien, which is acknowledged in the episode itself.
- When Colonel Samantha Carter mentions that she has experience with sleep deprivation, she is referring to the events of the episode "Morpheus". She also references events in "Cold Lazarus" (the crystal-based life form that took the form of Colonel Jack O'Neill) and "Entity" (the alien life form that took control of her body.)
- The device used to allow Sheppard to enter McKay's dreams was an adapted version of the virtual reality pods used in the Stargate SG-1 episodes "The Gamekeeper" and "Avatar".
- Fans who used iTunes to download the Atlantis season premiere "Adrift" discovered that they had in fact purchased this episode instead, three weeks before it was set to premiere on SciFi Channel. The mix-up likely comes from the fact that "Doppelganger" was the first episode of the season to be filmed, and thus carries an internal production number of 401 at the studio.
- This episode is the main reason why the Region 2 DVD volume release was given a "15" age restriction rather than the standard "12", due to its excessive violence in one particular scene. This was the only volume in the entire Stargate: Atlantis series to ever receive such a high age restriction.
- When the group is walking in the forest at the opening Sheppard say that he thinks they might be there because "somebody sitting in their nice cozy room typing on their computer sent them there for their own amusement". This is an obvious tongue in cheek dig at the writers who wrote this scene for the actors to slog through the underbrush.
- During the scenes with both Sheppard and the entity in them, it's possible to tell them apart as Sheppard is wearing a sweater while the entity is wearing Sheppard's uniform jacket.
- In the novel Stargate Atlantis: Homecoming, Teyla reveals that she conceived her son Torren John Emmagan shortly after this episode while grieving over the death of Dr. Kate Heightmeyer.
- In the scene when Ronon Dex walks through the door into the forest, you can clearly see that there was CGI involved. When you look at the big tree on the left side, it does not move right when the camera angle turns.
- When Ronon is hit by the vine while running in the forest, you can briefly see the person holding the other end of the vine, hiding behind some trees.
- In the scene where Dr. Jennifer Keller goes to the medicine cabinet for sleeping pills after her nightmare about Lt. Colonel John Sheppard, she opens the cabinet door partially before actually unlocking it.
- The sleepwalking Major Evan Lorne demands Sheppard and Colonel Samantha Carter be shot with an Anti-Replicator guns to prove they aren't Asurans. However, ARGs have been rendered useless as the Replicators are now immune which Lorne would know.
- When Sheppard and Dr. Rodney McKay look back at the clown in the boat, Sheppard's hair changes between shots.
- Hungarian: A hasonmás (The Doppelganger)
- German: Doppelgänger (Doppelganger)
- French: Cauchemar sur Atlantis (Nightmare on Atlantis)
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