The episode starts in the Gate Room with the announcement of an "Incoming traveller" as General Hammond stands by the base of the ramp, clenching and unclenching his fists. SG-1 appears through the Stargate, dressed in ponchos and quite obviously soaking wet. Hammond accuses them of being overdue. Jackson tells Hammond that the planet was not Kheb, as he'd hoped, and there was no sign of Sha'uri's Harsesis child. As the general orders the team to the infirmary there is an announcement over the loudspeakers warning of a hazardous materials transfer; reaching the elevator, SG-1 finds a guard there to escort them to the infirmary as a precaution, as there had been a tetrachlorethylene rupture on level 23.

Once in the infirmary, the team discusses the Harsesis child; as there are more announcements and alarms relating to the chemical spill, the nurses and Dr. Fraiser, performing their post-mission physicals, inject each of them with a yellow liquid that knocks them out. As Fraiser throws back the curtain that had been shielding herself and Carter, she tells the others, "Let's begin." A short time later, Teal'c awakens and overhears a conversation between Hammond and Fraiser, whom he can see with Sergeant Siler and an alien being standing close by. Fraiser tells Hammond how a large amount of sedative was needed to knock him out due to the "dominant parasitical species" of this world, and that Carter's body chemistry is also altered. Siler is ordered to take Teal'c to level 16 as the Jaffa feigns unconsciousness; reaching their destination, Teal'c knocks Siler out and hides him in an empty room before going to the Armoury and arming himself with a zat gun. Back at the elevator, Teal'c knocks out another SF who has just come off the elevator with Carter's unconscious body, and also the guard in the elevator. En route to another floor, Carter wakes and wants to know what's going on, initially disbelieving when Teal'c tells her what he overheard in the infirmary and states that Fraiser and Hammond "are not who they appear to be." He believes that there has been an alien incursion of the SGC, for he has seen one of the aliens himself. Wanting to know what has happened to O'Neill and Jackson, the two head for the security room, where they zat the female officer on duty and try to call up the security cameras on level 23, the supposed site of the chemical spill; however, not a single camera is working on that level. Hearing the announcement for an incoming traveller, Carter calls up the Gate Room, where O'Neill, Jackson, and Hammond are greeting aliens. Teal'c points out that the men they knew would not welcome aliens so politely, and the two of them determine that the people they see on-screen must be imposters. Meanwhile, two SFs find the unconscious guards in the elevator; one goes to inform General Hammond, while the other pulls down one of the unconscious men's shirts; underneath, there is an alien device attached to his chest.

Carter and Teal'c decide to leave the SGC and are about to make their escape when the alarm sounds. Teal'c informs Carter that he will buy time for her escape and she promises to come back for him, of which he has no doubt. She exits through the hatch and Teal'c knocks out two guards as a third shoots at the Jaffa, wounding him; Teal'c zats him. Outside, Carter has made it to the surface and heads into the surrounding woods, obviously still woozy from the sedative. Still in the SGC, Teal'c manages to disable two more SFs before the blast doors are lowered at either end of the hallway, sealing him inside with a gas canister; with no way out, it's not long before he succumbs to unconsciousness.

At a payphone outside an airport, Carter places a call to Colonel Maybourne, informing him of a possible foothold situation and asking him to meet her at an outdoor cafe near NID headquarters at 4pm. When he reminds her that she is "way outside your chain of command," Carter repeats that they have a foothold situation and that she believes that chain of command to be compromised; Maybourne agrees to meet her.

Back at the SGC, Teal'c is strapped down to a gurney. Fraiser asks him how he's feeling and explains that he "went a little crazy"; apparently, all of SG-1 was exposed to the fumes from the chemical spill the moment they got on the elevator. Teal'c became delusional, sprung Carter, and off the two went. Hammond appears at this point, wanting to know where Carter is: she, too, had an adverse effect to the chemical and is suffering from hallucinations and paranoia. When Teal'c claims to not know where the major is, Fraiser attempts to persuade him into sharing the information by telling him that her symptoms will only get worse; in fact, she could die.

At the outdoor cafe, Carter meets with Maybourne as planned. She says that she's not sure how many people have been compromised, but if they'd gotten to General Hammond.... Maybourne responds by telling her that the general sounded fine on the phone, just concerned about Carter. She's upset with the colonel; after all, she did say that they had a foothold situation. Maybourne, however, says he finds a chemical spill causing paranoid delusions infinitely more plausible than aliens taking over the SGC, and Carter moves to leave when O'Neill and Jackson appear on either side of her. Carter accuses Maybourne of being an idiot for informing them of her whereabouts, but eventually sits back down, where her teammates tell her that they'd all been affected by the tetrachlorethylene without even realizing it. Carter is adamant that she knows what she saw, at which point O'Neill asks her the side effects of being exposed to the chemical. The major seems somewhat disheartened as she recites what she knows -- hallucination and paranoid delusion -- but points out that "Dr. Fraiser injected me with something." O'Neill explains that the doctor was trying to sedate her but it didn't work on either her or Teal'c, who was fine by the way. Carter turns back to Maybourne and reiterates that he should have followed procedure. The colonel has his own plan, however; he will accompany them back to the SGC himself to ensure that all is well, and if he doesn't report back to his people then "action will be taken." Maybourne obviously believes that she is suffering the effects of a chemical spill; the fact that they are having such a private conversation in such a public place, he says, is a clear indication that Carter is a security risk in her present condition. He even threatens to handcuff her if she doesn't accompany them willingly. Obviously shaken by her teammates' assertions that she is merely hallucinating, Carter reluctantly agrees to come back with them to Cheyenne Mountain.

Still in the infirmary, Teal'c asks to be released from his bonds, but Fraiser refuses on the grounds that he may have a relapse; three of the men he attacked earlier have concussions. In the background, Hammond answers the phone; Carter has been located. Fraiser, listening to the general's end of the conversation, looks at Teal'c as she says that they "may begin experimenting immediately."

Aboard the NID plane, O'Neill returns from his phone call informing Hammond of their eventual arrival. He assures Maybourne that the chemical spill has been cleaned up, but as he speaks he "flickers", appearing for an instant as an alien. Carter immediately grabs Maybourne's gun and holds it on O'Neill. Jackson thinks she's hallucinating again; as she focusses her attention on the archaeologist for a moment, O'Neill stands to attack her and she shoots him twice in the chest. He falls back and turns into an alien, and Carter turns her weapon on Jackson, who looks stunned. From the plane's cockpit, Major Davis exits and fires his gun, his mouth wide open and emitting an unnatural, almost electronic noise. Carter shoots him twice in the chest and he, too, turns into an alien. Maybourne then orders Carter to check the pilot, to see if he's who he's supposed to be, but the major tells him to go first. Maybourne pulls out a Swiss Army knife and slices his hand, revealing blood, and asks if that's proof enough. Carter hands him the weapon and heads for the cockpit, picking up "Davis's" gun as she passes by the dead alien.

On level 23 of the SGC, O'Neill awakens and finds himself suspended above the ground in a harness, a headband above his brow. Around him various other people are also suspended, unconscious.

On the plane, Carter removes a device from the head of the alien who had been posing as O'Neill as Maybourne accosts Jackson, wanting to know what it is and how it works, but Jackson maintains his innocence. From the alien Carter removes another device, this one identical to the one found on the unconscious guard in the elevator, then checks Jackson's chest where she finds another one. Removing it, Jackson, too, is revealed to be an alien. Carter then puts the device on her own hand, at which point her appearance changes; she now looks exactly like Jackson. The imposter moves to attack her but Maybourne shoots him, wounding but not killing the extraterrestrial. Removing the device, Carter informs the colonel that the device creates an image but she couldn't hear any of Jackson's thoughts, and surmises that that's the purpose of the first device she pulled from the alien's head. She then begins to wonder why the image blinked out and hypothesizes that it must be due to electronic interference -- the noise from the plane's engines. If she can replicate it, she says, then they will be able to determine who is an alien and who isn't.

In the room on level 23, a second person awakens: Major Davis. He and O'Neill try to figure out what's going on, but a double of Fraiser enters the room -- the real Dr. Fraiser is strung up alongside them -- and they must feign unconsciousness. As O'Neill watches through slitted eyes, the doctor and an alien put a person through a machine of some type and then string him up with the others as Fraiser places two devices on the alien; the alien then takes on the appearance of the man who had just been suspended. She hesitates just as she's about to leave, looking up at O'Neill with suspicion. He closes his eyes quickly and she watches him for a moment, but leaves without doing anything.

Back in the infirmary, Fraiser is experimenting on Teal'c's Goa'uld larva without the benefit of anesthesia. Hammond orders her to take the Jaffa back to his holding cell; Carter will arrive soon, and she may be less resistant.O'Neill and Davis manage to free themselves from their harnesses and drop to the floor, guessing that if Fraiser has a double, they must also; but why are they awake and not the others? O'Neill decides to try waking Fraiser. He removes her headband but an alarm sounds, and in the infirmary the doctor's double halts, looking disoriented. O'Neill quickly replaces the headband and hopes that no one heard the alarm, but Fraiser's double soon arrives. She looks up at the people hanging from the ceiling but finds nothing amiss; the real doctor is still unconscious. The colonel, hiding behind the door, knocks out the imposter when she turns to leave as, aboveground, Carter returns to the hatch through which she'd escaped; before entering, however, she places the alien device beneath her shirt and takes on Jackson's image.

O'Neill and Davis check over "Fraiser" and find an alien weapon and another of the devices on her chest; when O'Neill removes it, she's revealed to be an alien. At this point Carter, disguised as Jackson, enters the room, where after some confusion about who everyone really is the major explains what has happened and that Maybourne will be arriving in less than half an hour with reinforcements to take back the base. They surmise that O'Neill and Davis must have awoken when Carter killed their doubles on the plane, and she tells how she has a device in her lab that will emit the precise frequency to disrupt the aliens' projected images. She goes to her lab while O'Neill and Davis go to the Armoury; after arming themselves, O'Neill frees Teal'c by pretending that he is one of the aliens and zatting the guards on duty. In her lab, Carter finds the correct frequency to disrupt the images. Hammond enters and she tries the sound on him; once revealed to be an imposter, "Hammond" knocks Carter across the room before he is summoned to the Control Room. Carter turns on the loudspeaker and sends the sound throughout the entire base so that the aliens will all be exposed for who they are.

In the Control Room, the aliens use the security monitors to see that O'Neill and Teal'c are free and dial up the Stargate. Carter meets up with the two men in a corridor, where she tells the colonel that they can't allow the aliens to escape because they've had access to their minds and know everything about them. The three SG-1 members go to the Control Room and Carter shuts down the 'gate, but not before several of the aliens have escaped. Unable to leave the planet, the rest of the aliens all self-destruct, causing a lot of damage to the Gate Room.

In the Debriefing Room, Hammond informs SG-1 that P3X 118 has been locked out and all the codes have been changed. All of the humans woke spontaneously when the aliens self-destructed; even those not caught in the explosion died. The whole incursion began when the aliens came back posing as SG-6; the rest of the base was duplicated and Major Davis was summoned by Hammond's double, the Pentagon being next on the aliens' agenda. Carter says that a high-frequency blast from a harmonic generator each time a team returns should prevent it from happening again.

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