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. Tom’s decision to have the rebel skitters fight alongside humans creates tension and raises suspicions that someone may be feeding secrets to the enemy. Meanwhile, Hal struggles with nightmares that seem so real, he has difficulty knowing if he’s awake or dreaming. And Tom and Anne prepare to welcome their baby.

With hostilities escalating between the resistance and the alien invaders, Tom calls on a nuclear specialist known as "The Rat King" to come up with a plan that will strip the aliens of their power. As suspicion continues to mount about a mole within the resistance, Tom and his leaders make a drastic decision that jeopardizes trust among the group. Anne, meanwhile, has a feeling that all is not right with her newborn.

The two-year anniversary of the alien invasion is fast approaching as the people of Charleston prepare for another potentially devastating offensive. A sniper attack by an unlikely gunman creates questions and doubts within the new government. Hal believes he knows the identity of the mole. And Anne’s concern for her baby continues to grow.

After the people of Charleston defeat another alien attack with the help of new advanced weaponry, Tom is invited to meet with a powerful leader. While Hal wrestles with an invasive evil, Ben struggles with his identity and the notion of being human again. And Anne uncovers startling new information that puts everyone in jeopardy.

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. And Marina takes matters into her own hands in Charleston, disregarding Tom’s authority.

Hal finally reveals his internal struggle to everyone, and it doesn’t bode well for the Masons. Lourdes experiments with a risky new medical procedure. And Charleston’s government sees a massive shift in leadership when a group breaks away on a search and rescue mission.

The Masons run into trouble on the road when a family of outlaws intercepts their search-and-rescue mission. Meanwhile, looming doubts over the construction of a massive alien weapon ignite a conflict of interests. And an investigation to apprehend a killer on the loose hits a road block.

Things seem much too calm for Tom, making him suspicious of his surroundings. On his way back to Charleston, he makes a number of discoveries, some incredibly surprising and others utterly horrifying. Meanwhile, Weaver and Pope butt heads over how to handle the suspected mole.

Tom uncovers confidential intelligence about the heart of the alien operation. Meanwhile, Charleston prepares to mount an offensive against the Espheni, but a massive explosion brings the operation to a halt. And the identity of the mole is finally uncovered, but not before more blood has been shed.