Part 1 follows on from The OMAC Project #3. Superman returns to his new Fortress of Solitude in the Amazon forest with blood on his hands and no clear recollection of who it belongs to. He remembers going to meet hs wife, Lois Lane, in her office only to find her with Brainiac. There follows a long drawn out fight ending with him back in the Fortress where he realises that the blood cannot belong to Brainiac. Members of the JLA arrive and ask him to return with them.
Part 2 With the prompting of JLA members, Superman remembers the meeting with Lois Lane differently – as a long drawn out battle against Darkseid. The JLA make him realise whose blood is on his hands and he travels with them to the Watchtower where he finds a badly beaten Batman in the infirmary.
Part 3 As Batman heals, the JLA show Superman the Watchtower recordings of him attacking Batman. A telepathic probe by the Martian Manhunter and Wonder Woman reveal Maxwell Lord’s responsibility for Superman’s actions. While willing to be helped at first, Superman becomes convinced the JLA are the ones who are brainwashed and battles them before escaping. Wonder Woman follows him to the Checkmate Castle in Switzerland where Superman – under the control of Max – captures her.
Part 4 Under the influence of Maxwell Lord, Superman is convinced that Wonder Woman is Doomsday and that she has killed Lois Lane. They fight before Wonder Woman escapes from him and returns to the Checkmate castle and confronts Lord again, capturing him with her lasso. Unable to refuse her demands while tied up in it, Lord releases Superman from his control. When Wonder Woman asks Lord how to free Superman completely from his control, Lord replies that she must kill him. After only a moment’s thought, she does just that, breaking Lord’s neck with a twist of her hands. The story continues in The OMAC Project #4.