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.

When the 2nd Mass destroys a crucial Espheni base, a relentless enemy is taken down and the Mason family is reunited with those who had been lost. But the arrival of more interstellar players puts the fate of the Earth’s remaining survivors in doubt.

Tom's life hangs in the balance as his beamer drifts into space. Tom encounters a surprising guest.

A surprise skitter attack leaves the 2nd Mass without food. In desperation, Maggie, Ben, Pope, and Sara go on a dangerous mission hoping to find supplies.

The 2nd Mass discovers the source for the seemingly endless supply of enemy forces. Hal disobeys his father.

A mission to procure vehicles and fuel goes awry, and a desperate Pope takes things into his own hands. Cochise shares troubling news with Anne.

The 2nd Mass leaves Chinatown en route to what they hope will be the final Espheni battle. Along the way, they encounter a deranged and desperate gunman who takes a hostage. Meanwhile, Tom sets off to rescue Hal.

Injured, Tom takes refuge with a unique family who has distanced themselves from the fight, giving him a glimpse of life without war. Hal and Isabella's romance grows as they search for a missing Tom. Meanwhile, The 2nd Mass locates an Espheni device that could be a linchpin to winning the war if they can figure out how to use it. And Maggie makes a decision that has consequences for her and the entire 2nd Mass.

The 2nd Mass arrives at a safe haven. As the two groups make plans for the final assault on the Espheni, the 2nd Mass begins to realize that things aren't exactly as they seem.

Weaver discovers a shocking truth about an old friend and must decide how to best protect the 2nd Mass. Maggie and Isabella are forced to work together.

Tom gains a powerful new weapon. Ben puts his life on the line to extract enemy plans. Pope discovers that Tom is alive. Meanwhile, the 2nd Mass must reassess their situation when an unexpected visitor appears.

The final standoff brings the Masons, the 2nd Mass, and their new allies into the bowels of an iconic American location, wrought with new and unpredictable obstacles. Despite great loss along the way, they must persevere with hopes of once and for all reclaiming Earth and humanity.