Phantoms: After the team makes the grisly discovery off-world that Major Leonard killed his own men because they were all seeing hallucinations caused by a device, the device begins creating hallucinations in Sheppard's team, who see each other as enemies!

The Return Part 1: When McKay, Sheppard and the others discover an Aurora-class warship called the Tria filled with Ancients, they're ecstatic. But with the return of the Ancients to Atlantis, the humans are ordered to leave, forcing the four good friends to go their separate ways.

The Return Part 2: Major General Jack O'Neill and Richard Woolsey are currently in hiding from Replicators. But their hopes of escape increase one Sheppard's team hears of the attack on Atlantis, and goes AWOL in hopes of regaining control of the city.

Echoes: When the whales of Lantia gather around city, the people of Atlantis begin to fall seriously ill. Meanwhile Teyla and others begin to witness what appear to be ghosts of the Ancients.