The movie opens with Manchester Black watching news stories about villains and how they’re given second chances. All of the news stories come down to one subject: the world wants solutions to all of the evil in the world – by killing it. When Manchester sees this, he turns off the TV and begins his plot to keep the world safe by any means necessary.
Back at Metropolis, Lois and Clark witness the death of multiple people in the streets at the hands of the Atomic Skull who was killing people to draw out Superman. As the battle erupts throughout most of the city, Superman ends up defeating Atomic Skull by throwing him into a lake. After this, Superman gives a speech at the United Nations about the greater good that is found within everyone. During this the leaders of Bialyia and Pokolistan begin to fight due to their peace treaty being broken, Superman leaves the United Nations to stop their armed forces from destroying each other.
As Superman arrives in Bialya, the Pokolistani forces release a bioweapon on the Bialyan military which destroys most of their ground forces. As Superman gets the soldiers to safety from the bioweapon, the Elite arrive just in time to help Superman destroy it.
Superman returns to Metropolis to report the news and also gain more information on the Elite. Superman and Lois fly to England to find out if they, and the world, can trust the Elite. It is revealed through Manchester Black that he gained his powers near puberty and used it for the first time to save his sister Vera from being hit by a train.
Through telepathy, Black gets a painful headache of multiple people screaming. The Elite and Superman arrive on the scene to save the civilians on a subway train which was trapped underwater due to a terrorist attack. After Superman and Black save the passengers, Black interrogates the terrorists that bombed the train nearly killing them. Superman begins to be concerned about the motives of his new-found friends.
Back in Metropolis, Clark and Lois talk about the information they had found on the Elite and Manchester Black’s history. Lois tells Clark that there is no birth record or death certificate of Manchester’s sister Vera. This makes Clark further question the Elite’s origin and what they are really trying to accomplish. When Manchester broadcasts a message for all the world to hear, he ends up telling them that they will take care of all the bad guys in the world by killing them.
After the broadcast, Superman returns to the Fortress of Solitude to search for reliable information on the Elite. Having failed in finding information, Superman travels to Bialya. While there Superman is hit by an EMP which weakens him. Closing Pokolistani forces are about to attack him when the Elite attacks. Powerless to stop the chaos that the Elite inflict on the Pokolistani military, Superman ends up passing out. He eventually awakens at the Elite’s base of operations, a sentient macroorganism called Bonnie, and is teleported back to Earth after he fails to convince the Elite that they don’t have to kill to be heroes.
In Metropolis, Atomic Skull breaks out of prison and looks for revenge on Superman. The Elite arrives but have little success against the overpowered Atomic Skull. When Superman arrives, he coordinates an attack with the Elite to get all the extra power away from Atomic Skull. After Atomic Skull’s power is drained by Coldcast, he is executed by Manchester Black under the vote of a boy whose father was one of Atomic Skull’s victims.
After protecting Pokolistan from Bialya’s jets, Superman is visited by the Elite who tell him that they have killed both the Pokolistanian and Bialyan leaders and that peace can reign supreme in that area once again. Angered by Manchester’s uncontrollable urge to kill the villains, Superman punches him in the face and the Elite take it as a statement of war against the world’s “favorite heroes.” They tell Superman that they will kill him for this outrage.
The next day, Superman stands in the middle of Metropolis telling the Elite that he is ready to fight. Asking them to do it somewhere safe, they teleport to the Moon where they begin their fight, with the people of Metropolis watching via Bonnie. Both sides are evenly matched until Black telekinetically induces a seizure in Superman. Coldcast then unleashes a massive blast of electromagnetic energy on Superman, and to those watching the battle on Earth, it appears that Superman has been obliterated. However, moments later, the Elite start hearing Superman’s voice all around them. In his taunts, Superman states that he has finally been convinced that he needs to start killing villains–beginning with the Elite. Superman then begins to take out the Elite one by one; first he injects Menagerie with a poison that causes her sym-beasts to abandon her and apparently kills her. The Hat attempts to exploit Superman’s known weakness to magic but is suffocated by a super-speed generated whirlwind and sucked into the funnel.
Against Coldcast’s wishes, Manchester teleports them to Metropolis to use the innocent civilians as cover. Black gives the order to combine powers to destroy Metropolis when Superman appears. After Superman knocks Coldcast into orbit, he confronts Black. Manchester attacks Superman with everything he has but fails to harm the Man of Steel. Through heat vision, Superman lobotomizes Manchester, stripping him of his powers. Believing his death to be seconds away, Manchester tells Superman that the world knows he is no better than they are and will never again trust him. Superman reveals that he faked killing the other members of the Elite and had his Super-Robots protect all of the civilians present to and create the illusion that he had killed indiscriminately. They were really transported to the Fortress of Solitude to be stripped of their powers, then sent to a prison. In addition, Bonnie was offered a way to return home. In the end, the people of Earth see that Superman’s way is best for all of mankind. After that, he flies off with Lois and they kiss.