Seven months following the events of season two, the 2nd Mass has made Charleston into their home. Tom has been elected president of the new United States, and humanity has begun to make headway against its otherworldly enemy. The main reason for this is the arrival of a friendly alien race called the Volm, which have a standing grudge against the evil Espheni. Meanwhile, the hunt is on for a spy in the colony, and Hal is plagued by strange dreams.
A little bundle of joy arrives in Charleston, as Tom and Ann celebrate the birth of their daughter Alexis. All is not happy however, as battles between humanity and the Espheni continue to escalate. In a desperate bid to cut off an enemy power source, Tom enlists the help of an reclusive nuclear scientist named Dr. Roger Kadar. Elsewhere, the spy takes out of a member of the colony, and Hal's dreams of Karen intensify.
With the two-year anniversary of the Espheni invasion looming on the horizon, the 2nd Mass finds itself under attack from an entirely unexpected threat. Elsewhere, Anne becomes more and more worried that her baby may not be entirely human, but Lourdes suspects it may simply be postpartum psychosis. Also, Hal begins to suspect he himself might be the spy everyone is looking for.
Following a successful defense of Charleston from an Espheni attack, Tom joins new arrival Lt. Fisher, Gen. Bressler, Pope, and Volm ally Cochise on a top secret mission to make contact with still living U.S. President Benjamin Hathaway. Meanwhile, Anne has DNA tests performed on Alexis, Hal fights to keep control over his own mind, and Ben can't decide whether to remove his harness spikes or not.
Tom awakens after the plane crash to find Bressler dead, and Pope unconscious. Tom drags Pope to safety, but both men are now stranded far from Charleston, with the Espheni on their tails. Back at camp, Weaver leads a search party looking for Anne and Alexis. Marina and Dr. Kadar grow steadily more suspicious of the Volm's secret weapon.
Tom demands to head out on a rescue mission to find Anne and Alexis, but before he can go, Hal's dark side finally makes itself known publicly. The implant controlled Mason takes his dad hostage, leading to a tense stand-off. The rebel skitters offer a risky solution to Hal's problem, one he may not live through. Also, Charleston's government experiences a major shake-up.
The Masons journey to rescue Anne and Alexis is interrupted by a surprise attack. A family called the Picketts robs and threatens them, leading to a family vs. family battle over the Masons' needed supplies and horses. Meanwhile, suspicions about the Volm weapon intensify, a barely alive President Hathaway is returned to Charleston by Cochise, and the true identity of the mole is revealed.
Tom awakens to find himself in a world he doesn't understand. Tom's wife is alive, and the invasion never happened. Everything seems perfect, that is until Tom begins receiving messages from someone named Anne Glass. Is Tom's dream world real, or simply Espheni mind games? Meanwhile back at Charleston, Pope and Weaver differ on how to handle the hunt for President Hathaway's killer.
Tom returns to Charleston, complete with new information on where the Espheni are vulnerable to attack.
Sadly, he also informs that Anne and Alexis are believed to be dead. Things are thrown into chaos when first the Volm complex and then Charleston are damaged by large explosions. Can Tom finally figure out the identity of the mole before it's too late?
The 2nd Mass celebrates a crucial victory against the Espheni, only to be shocked by the new plans of their allies the Volm. The advanced alien species has decided to ship humanity off to camps in Brazil, for their own safety. Naturally, Tom, Weaver, Pope and crew are having none of it. Also, Tom wages a final battle with Karen, and learns a shocking truth about Anne and Alexis.