With Weaver leading several squads of fighters against the aliens, Tom remains behind to help protect the civilians as they evacuate. But a major breach in security endangers both the soldiers and the civilians. Tom is confronted with a decision that may lead him to discovering what the aliens want with the captured teenagers, humankind and the planet.
As the 2nd Mass. prepares for a major assault, divisions within the ranks threaten to tear the group apart. Tom has difficulty processing the profound implications of Anne’s latest discovery.
The 2nd Mass prepares to take the fight to the invaders with an assault on one of their bases. But Weaver’s increasingly strange behavior worries Tom that he might not be fit to command. Hal and Tom encounter a left-behind woman (guest star Blair Brown, Fringe) who employed a suspicious means of surviving the invasion, making it unclear whether they can trust her.
Hal takes the lead fighting an unexpected threat against the children of the 2nd Mass. Anne has her hands full when Sarah goes into labor while the 2nd Mass base is being evacuated. Henry Czerny (The Tudors) guest stars.
Lt. Terry Clayton (guest star Henry Czerny – The Tudors) of the 7th Mass arrives with word that the aliens are on their way to attack the 2nd Mass. Clayton’s plan to lead the children to a safe haven while the adults remain behind to fight is met with some resistance from the parents, including Tom.
Hal comes up with a risky new plan to rescue captured teenagers from the aliens, but it might require putting someone at risk. Meanwhile, a sudden tragedy causes Anne to make an enormous discovery that proves instrumental to Hal’s risky plan.
Tom and his team head out to track down more motorcycles for the 2nd Mass., relying on Pope to guide them to a good location. They hit the jackpot until they meet some skitters and harnessed teenagers at the bike shop. Back at the base, Dr. Harris (guest star Steven Weber) and Anne disagree over the best method to gather more intelligence on the aliens.
Dr. Michael Harris (guest star Steven Weber – Happy Town) joins the 2nd Mass with a theory about what might save the teenagers abducted by the aliens. But the plan could be derailed when Tom starts digging for answers to questions that have haunted him since the early days of the invasion. The 2nd Mass comes face to face with skitters and mechs when they attempt to rescue Ben.
While scouting for supplies, Tom, Hal and their squad encounter a gang of marauders determined to get their hands on the 2nd Massachusetts’ weapons. Leading the gang is an ex-con named John Pope, who decides to use his hostages as bargaining material.
The world is left in tatters after a sudden, unprovoked and unexplained invasion by aliens, leaving the planet’s remaining human population to fight for survival against the occupiers. History professor Tom Mason (Noah Wyle - ER) has been named second in command for the 2nd Mass, but his real focus is on his three sons, one of whom has been captured by the aliens for an unknown purpose.
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. And Tector embraces his military past.
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.
While on patrol together, Ben and Hal try to help a young boy and wind up having their bikes stolen. The hunt to recover them leads them to the discovery of something much bigger. Also, Matt is put in danger, and Weaver is reunited with a family member.
The 2nd Mass moves into an airport hanger, but the drafty conditions cause Anne to grow concerned about the group’s health. Meanwhile, the Berserkers hatch a plan to get rid of Tom. And while dealing with a loss of one of its own, the 2nd Mass receives a promise of hope from a mysterious visitor.
Tom is still haunted by memories of his time with the aliens and begins to wonder if they did something to his mind. Pope, who is in charge of questioning Tom, plants seeds of doubt about him among the group. Meanwhile, Ben’s hatred for skitters grows, and the 2nd Mass scouts locate an old bridge that will help them cross the river to safety ahead of an impending attack.
Three months have passed since Tom Mason agreed to go with the alien invaders. Weaver is still in command of the 2nd Mass, while Anne continues to serve as medic. They have seen many battles and are a much leaner unit now. Pope has taken command of the Berserkers, a renegade group within the 2nd Mass that Weaver doesn’t fully trust. When Tom suddenly returns, he is faced with doubt about his loyalties to the group. Meanwhile, Hal and Ben continue to drift apart as Ben challenges his older brother’s authority.
