3 months after Tom has gone aboard the alien ship Hal and Ben are still helping to protect the remaining members of the 2nd Mass under the command of Captain Weaver while continuing the search for their father. Meanwhile Matt struggles to find his place in the world and Anne takes a more maternal role with the Mason boys.

Tom is plagued by haunting memories of his time with the aliens and begins to speculate that they may have tampered with his mind. Elsewhere, Pope oversees an interview with Tom; Ben's hatred toward the skitters escalates; and scouts discover a bridge that could lead the group to safety.

The unit moves into an airport hanger, but the relocation could cause health problems. Elsewhere, the renegade Berserkers scheme to cast out Tom; the unit copes with a loss; an enigmatic visitor provides hope.

Ben and Hal go on patrol and help a boy, only to have their bikes stolen. The subsequent search for the bikes leads to a major discovery. Meanwhile, Matt steps into a dangerous situation; and Weaver reconnects with a family member.

A familiar person returns to the unit, but his motives are scrutinized. Elsewhere, a captured skitter is imprisoned at the camp, and Hal connects with Maggie as she casts light on her past.

While on patrol, Hal and Maggie discover an unharnessed and alive Karen among a group of half-buried unharnessed inactive persons. Tom has some tough decisions to make when Weaver falls gravely ill from the bite he received at the harnessing factory.

Tom lands himself another captive andBen is lead into danger at the hand of someone he trusts. The unit faces a brand new enemy while trapped in the basement of a building.

En route to Charleston, the 2nd Mass continues to grieve for the group's recent losses. Matt bonds with a new harnessed girl and Weaver learns more about Tector's history.

Tector makes the decision to embrace his military past, while Maggie becomes suspicious that Pope will be leaving he group. The 2nd Mass continue to meet new people along the way, as Tom runs into a former untrustworthy mentor.

When skitters approach the newly combined resistance force, the groups' interaction surprises everyone. Meanwhile, Tom finds out life-changing news just as the 2nd Mass comes face-to-face with their most dangerous threat to date.