Following an international incident involving the Avengers that results in collateral damage, political pressure mounts for a system of accountability and a governing body to determine when to enlist the services of the team. The new status quo deeply divides members of the Avengers. Tony Stark, Iron Man, supports oversight as he feels remorse over the consequences of their previous battles and fears the unregulated actions of superheroes. On the other hand, Steve Rogers, Captain America, believes that saving the world is daring enough without the added complication of political interference and fears the potential corruption and manipulation of such a governing system.

This ideological split results in the fragmentation of the Avengers into two opposing factions—one led by Captain America who wishes to remain free from control to protect humanity without government restriction, and the other by Iron Man, who surprisingly chooses to support government oversight and accountability. As they recruit a number of other heroes to their causes, each side gears up for a confrontation, with friendships and partnerships put to the test. The divide is further complicated by the return of Steve's old friend, Bucky Barnes, the Winter Soldier, who is struggling with his past actions as a brainwashed Hydra agent and is being pursued as an international criminal for crimes he did not control.