Season 3 picks up with Layton and his inner circle commanding a small 10-car "pirate train" in search of Melanie and a possible warm location to restart civilization. Back on Snowpiercer, Mr. Wilford is consolidating power, awaiting Layton's return.

At the end of Season 1, the survivors of the revolution are trying to pick up the pieces and maintain a fragile peace amongst the now merged classes with Layton (Daveed Diggs) emerging as the train's leader. Discovering Mr. Wilford (Sean Bean) is alive and headed their way on a rival train, Melanie (Jennifer Connelly) risks going outside to prevent him from invading Snowpiercer. While she's out there, it's revealed that Alexandra (Rowan Blanchard), Melanie's daughter, who she thought had died, is alive and has become Wilford's dedicated protegee. In season two, an entirely new power struggle emerges, causing a dangerous rift as people are divided between their loyalty to Layton and to Mr. Wilford, who has a new train, new technology and a game plan that keeps everyone guessing. While Layton battles Wilford for the soul of Snowpiercer, Melanie leads the charge on a shocking new discovery that could change the fate of humanity.