Falling Skies tells the story of the aftermath of a global invasion by extraterrestrials (including the insectoid multi-legged beings known as "skitters," a race of humanoid gray-skinned beings that seem to be their commanders, and mechanical attack drones called "mechs") that neutralizes the world's power grid and technology, destroys the combined militaries of all the world's countries, and apparently kills over 90% of the human population, all within a few days. The invasion and the aliens' objectives are not explained, though the aliens try to round up children between the ages of 8 and 18 and attach a biomechanical obedience device onto (and into) their spines, referred to as a "harness." The harness controls the child's mind, and forcibly removing it instantly kills the child. The story picks up six months after the invasion and follows a group of survivors who band together to fight back. The group, known as the Second Massachusetts (an allusion to a historical regiment from the continental army), is led by retired Captain Weaver and Boston University history professor Tom Mason who, while in search of his son Ben, must put his extensive knowledge of military history into practice as one of the leaders of the resistance movement.

Even though the invasion comes from another world, the word "alien" is not said once in the entire series (it is said at least once, in episode 7 of season 1 "Sanctuary Part 2" at about 30 mins in, Hal says that they "are going to kick their alien a**es")