The game does follow the story of the movie, but inserts extra scenes in between those of the movie. As a result, Superman fights many of his known villains in the game.
Five years later, Superman has visited Krypton and learned that nothing remains of his home world. On his way back to Earth, he's intercepted by Mongul, who pits him against some of the galaxy's greatest warriors in his arena. Superman is able to defeat them, before taking on Mongul himself.
Upon returning to Earth, he begins protecting Metropolis once again. Metallo is attacking the city with robots, and Superman fights them off, before facing Metallo himself. Metallo manages to absorb a huge amount of technology, making a massive body for himself, which he begins using to destroy Metropolis. Superman defeats him, deflects a missile he fires at the city and apprehends him.
Superman continues defending Metropolis, battling numerous robot attacks, as well as natural disasters, fires, mutants, and monsters that attack the city. Superman has a final showdown with Mongul.
When Lex Luthor creates an artificial island off the east coast of the United States, Superman protects the city from the fallout -- a series of tornadoes which threaten to devour Metropolis.
Finally, he confronts Luthor and sends his island into space.