Phantoms

"Phantoms" is the ninth episode of the third season of Stargate Atlantis.

Plot
During an off-world mission, a team is overdue for contact, and Sheppard takes his team, Beckett, and three other marines to find them. Upon arriving, they find four Genii corpses that are seriously decayed&mdash;and who appear to have killed each other. Finding a cave with strange energy readings, they discover a Wraith bunker, including a damaged generator. Nearby are the bodies of the missing team, minus their CO, Major Leonard. A video recording indicates that Leonard killed his men, but one of them mentions requesting evac by the Prometheus. Deciding they need more help, the Team tries to get back to Atlantis, but someone has sabotaged the DHD to explode, which kills one of the marines. On top of that, they draw fire from Leonard, injuring the two other marines, Kagan and Barroso. Sheppard decides to head back to the cave.

While there, McKay deduces that the device is a Wraith generator designed to cause hallucinations in humans, increasing the Wraith's own hallucination producing ability. The Genii soldiers apparently found and activated it. Unaware of how to turn it off, they tried to destroy it, but only succeeded in damaging the device, and it will take McKay some time to turn it off. Ronon soon follows the hallucinating Leonard, with Sheppard and Teyla in pursuit, but Teyla is shot in the leg. Sheppard manages to get the wounded Teyla to Leonard's camp, and tries to dress her wounds. Leonard soon approaches but runs out of ammo. Sheppard tries to calm him down, but Leonard, thinking Sheppard is a Kull warrior, kills himself with a grenade.

Soon, the others are affected, and they start behaving unusually strange. Later even the team is experiencing weird things: Sheppard hallucinates that he is back in Afghanistan; Ronon believes there are Wraith nearby; Beckett believes that Barroso is still alive and that Kagan is dead, and Rodney believes the generator is on the verge of exploding. Teyla alone is unaffected due to the Wraith DNA in her genetic makeup. Believing Teyla is Captain Holland, a soldier who was wounded in Afghanistan, Sheppard takes her back to the cave, with Ronon, who believes that Sheppard is a Wraith trying to feed off Teyla, in pursuit.

At the cave, Beckett, at the urging of a hallucination of a dead Barroso, takes Kagan to find help, while McKay realizes that he is affected by the machine, but is then shot by Sheppard. A wounded Mckay tells Teyla how to deactivate the machine, and Teyla tells Sheppard what to do, saying it will allow them to be rescued. Sheppard deactivates the machine, and everyone immediately reverts to normal. Beckett is nearby, and Kagan is also alive. Later, with the Daedalus enroute, Teyla asks if Sheppard saved Holland, but he failed. Teyla comments that at least they are alive. While resting near the cave, McKay complains about how Sheppard shot him. So John tells him to get some rest. Ronon says that John shot him also. John says that he is sorry for shooting everyone.

Trivia

 * This is the first episode to detail Sheppard's "black mark" in Afghanistan.
 * This is the first appearance of Kull Warriors on Stargate Atlantis, though they are only hallucinations - and are only referred to as "super soldiers"
 * Throughout the Episode the model of Sheppard and Teyla's P90 is changed in certain moments from the standard FN P90 to the P90 TR.
 * Mckay references Spinal Tap in this episode when he states "Whoever turned it on, dialed it up to eleven, then just left it there". The joke in Spinal Tap is why do amplifiers go up to eleven and not just ten.