The story flows out of events outlined in Superman: Y2K, in which futuristic villain Brainiac 13 injected Metropolis with a technological virus. Superman was able to prevent it from spreading, but as a result of it, the city was upgraded into a true "City of Tomorrow". Huge high-tech buildings soar into the sky while hover cars and the Rail Whale bullet train travel throughout the city.

As the game begins, Brainiac 13 has decided to return to Metropolis and harvest the technology that is residing in the city. This results in massive chaos and danger that Superman must stop.