Survivors of an alien attack on earth gather together to fight for their lives and fight back.

The world has been invaded and destroyed by aliens and the survivors organize a resistance. In Massachusetts, the history professor Tom Mason is assigned as second in command of the 2nd Massachusetts regiment. He grieves the death of his beloved wife and tries to protect his sons Hal and Matt. He also plans to retrieve his son Ben that has been abducted by the aliens.

Tom and his team goes to seek out a weapons armory but they are captured by a gang of marauders led by Pope that demands food, weapons and vehicle to release the prisoners. However, Maggie, from the marauders group, saves them and joins the 2nd Mass while Pope is arrested..

Dr. Michael Harris joins the 2nd Mass to teach how to save the children captured by the aliens. Hal and Karen try to rescue Ben, but she is captured by the alien and Hal is forced to see the remaining kids killed by a Mech to deliver a message to the survivors. Tom succeeds to capture a skitter alive while Pope is promoted to the new cook of the 2nd Mass.

Weaver asks Tom to go to a motorcycle shop with Pope and his team to see if the acquire motorcycles and parts to repair their bikers. They see a nest of Skitters sleeping under a bridge, but Tom does not let Pope to attack them. They arrive at the shop and Pope flees and blows up the nest, attracting Mechs. Meanwhile in the school, Anne and Harris disagrees how to treat the Skitter made prisoner and Rick tries to defend the alien.

Hal comes up with a risky new plan to rescue captured teenagers from the aliens, but it might require putting someone at risk.

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.

Hal takes the lead fighting an unexpected threat against the children of the 2nd Mass.

The 2nd Mass. prepares to take the fight to the invaders with an assault on one of their bases.

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.

Rick flees to meet Megan and discloses the plan of the humans; however, she leaves him behind and Tom brings him back to the 2nd Mass. Captain Weaver requests volunteers to blow up the Skitter base since he does not have any information regarding Potter and the 4th and 5th Mass. Tom evacuates the civilians since the enemies know where they are. When they are attacked by Mechs, Scott and Ben jam their transmission. Tom finds Weaver and rescues him, but they are stopped on the road by Karen that invites Tom to meet her leader; otherwise the 2nd Mass will be destroyed.

Three months have passed, now mobilized the 2nd Mass. persists on the run without Tom, but a flaw makes them prey to attack. Tom sees the traps of good and evil on the long road home after fleeing, but questions of his escape go unanswered.

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.

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.

While on patrol together, Ben and Hal try to help a young boy and wind up having their bikes stolen.

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.

Season three of Falling Skies opens seven months after the 2nd Mass arrived in Charleston. In the interim, Tom has been elected to political office, but he has his hands full as the resistance continues to battle the alien invaders.

The 2nd Mass moves into an airport hanger, but the drafty conditions cause Anne to grow concerned about the group's health.

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.

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.

Karen and Ben stumble upon aliens and Ben learns why Karen returned home. But he is rescued by Tom and a team that capture an Overlord. The 2nd Mass is surrounded by the enemy and attacked by Skitters and Mechs. Trapped in the hospital, they see Karen offer to let them go free provided they release her Overlord. They do not accept and soon they find a new danger, the crawlies.

When a mission goes terribly awry, Tom and Pope must rely on each other to survive. Meanwhile, Weaver and company search desperately for two members of the 2nd Mass who have gone missing.

After the people of Charleston defeat another alien attack with the help of new advanced weaponry, and Tom is invited to meet with a powerful leader (guest star Stephen Collins).

Things seem much too calm for Tom, making him suspicious of his surroundings.