- Superman and Supergirl are working together to eradicate Intergang and are seemingly succeeding.
- Lex Luthor is back in the public spotlight and has - inexplicably and to the public anger of Superman - received a full presidential pardon for his previous crimes. He is running a number of business and charitable organisations all targeted at "making things right".
- A group of super-powered people, calling themselves The Elite, arrive in Metropolis and begin assisting - violently - with cleaning up Intergang.
- Superman is disturbed by their methods and confronts them.
- Manchester Black, the leader of the Elite, broadcasts a message to the world saying that governments and superheroes have let the world down and that those who commit wrongs should be violently brought to account.
- Lois Lane stumbles upon a story that links Intergang to world leaders - including the president of the United States. Her and Clark struggle with the potential repercussions of running the story - but Lois decides that the public deserves to know the truth and prints it in the Daily Planet.
- The world erupts in fury and Intergang takes full advantage of it, pledging to kill each of the world leaders involved in the Intergang plot.
- Superman and Supergirl go around the world attempting to protect the world leaders from the Elite.
- Eventually, the White House is attacked and Superman and Supergirl fail to protect the President and his administration. The Government of the United States is killed, and the Elite assume control.
- The Elite then set about targeting other known super-powered being in the United States, including Superman and Supergirl (cameos by WW, Aquaman, Flash, etc.).
- Lex Luthor contacts Superman and offers him assistance in bringing the Elite down, using Intergang technology. Luthor believes that the Elite have not received their powers naturally, but using the same alien technology used by Intergang. He fashions machines which can be used to rid them of their superpowers.
- The Elite are defeated, stripped of their powers and sent to prison.
One year later...
- Lois Lane receives an anonymous tip that the Elite were created and given their superpowers by Intergang.
- A presidential election is being held, Lex Luthor has nominated as an independent candidate and is currently leading the vote.
- Superman stops by Luthor's office. Luthor says its good to have Superman's trust. Superman says he doesn't trust him and will be watching him. Cut outside to a group of civilians chanting Lex's name, carrying signs saying "Lex for President" and "Lex: Stopping the Supers" etc.
Flashback to the end of the previous movie...
We see a shadowy board meeting of Intergang discussing plans with "the new boss". A hand pushes a document titled "Project Elite" out onto the table. Lex Luthor emerges from the shadows.