Superman accompanies his alternate self into the future, where they witness a reality forged by the FutureSmiths. This is the natural timeline of Cir-El, who is actually a creation of the FutureSmiths. In this timeline, Lex Luthor is responsible for the creation of Brainiac 12 – an upgraded variant of the original Brainiac.
Cir-El sacrifices herself to prevent this timeline from ever occurring. Superman fights with Brainiac and traps him within a fold in time. Now that the reality of the FutureSmiths has been erased, all of the super-hero counterparts to this timeline cease to exist.
Superman attempts to return to his own timeline, but finds himself trapped in an alternate reality whereby his birth-parents never rocketed him away from Krypton.