400 years in the future, set in the year 2415, Aeon Flux is a mysterious assassin. Four centuries after a virus nearly annihilated the human race, leaving only five million survivors in a utopian city called Bregna. Aeon is struggling to destroy the Goodchild regime led by its namesake, Trevor Goodchild, the ruler of Bregna and a descendant of the man who found a cure for the deadly virus. As instructed by the Handler, Aeon is assigned to assassinate Goodchild, but there are deeper secrets to be discovered, and conspiracies to be foiled.

As Paleoclimatologist named Jack Hall is in Antartica, he discovers that a huge ice sheet has sheared off. But what he does not know is that this event will trigger a massive climate shift that will affect the world population. Meanwhile, his son Sam is with friends in New York to attend an event. There they discover that it has been raining non-stop for the past 3 weeks, and after a series of weather-related disasters begin to occur over the world, everybody realizes the world is entering a new Ice Age and the world population begins trying to evacuate to the warmer climates of the south. Jack makes a daring attempt to rescue his son and his friends who are stuck in New York and who have managed to survive not only a massive wave but also freezing cold temperatures that could possibly kill them.