The season's plot focuses on the 2nd Massachusetts' discovery that a large community of survivors has formed in Charleston, their journey there, and their reception once they arrive. It also focusses on the discovery that the Skitters are themselves "harnessed" and mind-controlled by the invaders, but that some of them are resistant to the effects and are rebelling against their Overlords.
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. Terry O’Quinn guest-stars.
The 2nd Mass meets new faces, while Tom comes across his former mentor and professor Arthur Manchester (guest star Terry O’Quinn). But it's difficult to know whom to trust. Maggie begins to realize that Pope may not be sticking with the group very long.
The 2nd Mass pushes on to Charleston, but some are still grieving the group’s recent losses. Weaver learns more about Tector’s background before the invasion. And Matt begins to bond with a harnessed girl who was found recently.
Ben is placed in harm’s way by someone who he thought he could trust. Tom captures another hostage. Weaver offers Matt a job to lift his spirits and make him feel useful. And when members of the 2nd Mass are trapped in the basement of a building, the situation takes a turn for the worst when they find themselves faced with a new enemy.
Hal stumbles across bodies of de-harnessed kids and finds someone from his past. Tom and Anne grow closer. And Weaver’s health deteriorates just as Tom discovers he may have been keeping important matters from the group in order to protect them.
A familiar face returns to the 2nd Mass, but his intentions remain unknown. Meanwhile, a skitter is captured and brought back to the camp as a prisoner. And Hal bonds with Maggie as she begins to open up about her past.