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.
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.
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.
With hostilities escalating between the resistance and the alien invaders, Tom calls on a nuclear specialist (guest star Robert Sean Leonard) known as "The Rat King" to come up with a plan that will strip the aliens of their power.