It's been three months since Tom Mason last boarded the spaceship, while the members of the 2nd Mass are working without him. When Tom unexpectedly reappears, he begins to be questioned about his allegiance to the group.
As Tom is still plagued by recollections of the extraterrestrials, he begins to wonder if they tampered with his mind. Pope interrogates Tom and begins to make the group grow suspicious of him.
Anne is concerned about the 2nd Mass as they move to an aircraft hangar abounding in drafts, but they soon receive a message of hope from a visitor flying by. Meanwhile, the Berserkers plot a scheme to do away with Tom.
Ben and Hal try to come to the aid of a youngster while on patrol, but their bikes get stolen, and as they go looking for them, they stumble upon a shocking discovery. Weaver re-encounters a relative of his; meanwhile, Matt is put in jeopardy.
As the members of the 2nd Mass stumble upon a battlefield devoid of humans, they learn that the Skitters are up to something. Tom finds himself in a quandary when Ben asks him to trust the foe, Red Eye. Hal and Maggie get closer.
When Captain Weaver is incapacitated due to a terrible virus, Tom assumes command of the 2nd Mass. As Pope is brought back to the group after being injured in the field, he tries to alert Tom about the deceptive Karen Nadler, who pretends she has returned to join them.
The members of the 2nd Mass try to escape when they are attacked by extraterrestrial invaders. Captain Weaver retakes leadership of the group and provides Matt with a new job. Things take a drastic turn when the group gets stranded in a building's basement.
Despite their losses, the 2nd Mass proceeds to Charleston. Weaver learns about Tector's past, while Matt tries to connect with a harnessed girl.
When the 2nd Mass arrives in Charleston, Tom runs across his former mentor and professor, Arthur Manchester, but things take an unexpected turn when their appearance brings about more trouble.
The Skitters reach Charleston with a plan to wreak havoc on the whole place. Karen flees after infecting Hal. Tom learns that Anne is expecting his kid, while the 2nd Mass is confronted with a new race of extraterrestrial invaders.