Sheppard reports that Major Leonard's team has failed to report in and asks for authorization to investigate. They find several dead Genii, shot and stabbed repeatedly apparently by each other. The teams move through the forest and find a bunker with more dead men who've killed each other. They find an active organic Wraith generator device sending out a low-frequency EM pulse. The Genii shot it up but it's re-growing itself.
Teyla finds the missing team, all dead, but Leonard's body is missing. McKay finds a camera and the playback shows that the team found the dead Genii and the generator, and then opened fire on by what they believed were invading aliens. But the camera reveals that in fact they were hallucinating and Leonard killed his own men. Sheppard orders a retreat and they head for the gate with the dead team's corpses, but spot some alien creature in the woods. They get to the gate but when they activate the DHD it blows up, killing one man and injuring two others, Kagan and Barroso. Leonard sabotaged the DHD and then opens fire, but flees before Ronon can catch him.
There's no power to dial up the gate so they retreat back to the cave. McKay tries to decipher the workings of the generator and concludes the Genii turned it up to maximum. Ronon sees what he thinks is a Wraith in the woods outside and goes after it, unaware that it's Leonard. Teyla and Sheppard catch up to the hallucinating Ronon, and Teyla is injured by Leonard. Sheppard turns and briefly sees Teyla as a former comrade, Holland. He takes her to a nearby shelter Leonard set up. Leonard comes nearby and shoots until he's out of ammo. Sheppard approaches him but Leonard hallucinates a group of super-soldiers advancing on him. Leonard uses a grenade to blow himself up rather than be "captured."
Sheppard returns to Teyla but then start hallucinating again, hearing a jeep. Beckett is working on the dying man, Kagan, but he dies. Weir tries to establish contact with the team and has a UAV sent through, while Beckett looks on as Kagan comes back to life. Beckett is concerned that the generator signal caused him to hallucinate Kagan's death. McKay reveals the generator was a Wraith experiment to tamper with the minds of their prey, but the Genii tampering is causing it to run out of control.
Sheppard continues to hallucinate and he suddenly finds himself in Afghanistan near a crashed helicopter. An injured Holland is also there and as Sheppard gives into the hallucination, Teyla can only look on in horror. Ronon is similarly hallucinating, and he and Sheppard both see/hallucinate the UAV but don't recognize it. Ronon shoots down the UAV, leaving Weir out of options since the Daedalus is between Atlantis and Earth.
Beckett checks up on Kagan, who is "dead" again, and has Barroso help him try to resuscitate. They manage to revive Kagan but McKay needs his help. McKay points out that Barroso is long dead and Beckett realizes he's been hallucinating the man's presence alive.
Sheppard and Ronon both attack each other, seeing the other as the enemy in their respective hallucinations. Sheppard wounds Ronon and then takes Teyla with him to go after his "enemy."
Beckett is trying to help McKay but is haunted by visions of the "living" Barroso. Beckett goes to help Kagan as the generator goes into overload. Rodney runs out but there's no explosion, and he realizes he's hallucinating. Sheppard comes charging up and shoot McKay, and Ronon hears the gunshot. McKay tries to tell Teyla what's going on, and she tries to direct Sheppard to the cave. She gets Sheppard into the cave and have him pull the right cable, and he does it just as Ronon comes in to shoot him. Everyone is back to normal and they go find Beckett, who is with the barely-living Kagan. Sheppard contacts Weir and lets her know what's up, and that they can get by until the Daedalus arrives.