In the original book, he had only a minor role, as he was all part of a distraction plan the Mutant had set up for Skipper Matthews. He was disguised as the Mutant, and was melted by a Molecule-Melter.
In the video game, Magnificent Molecule Man has a more significant role. He appears to be working for the Mutant, but there is more to him than meets the eye. Beforehand, he had imprisoned the Mutant's second-in-command, Chin Chilla, inside a comic book. Then he saves the Galloping Gazelle by knocking him into an elevator. The Masked Mutant is infuriated and chases after Molecule Man. In spite of everything, the Mutant catches up with Molecule Man and splits up his atoms. The player rejoins his atoms, making Molecule Man whole again. When he discovers Chin Chilla has escaped, he flees the scene, leaving the player to finish off the frosty freak.
Later, he appears in a meeting with the League of Good Guys. The superheroes question about his true potentials, but Molecule Man explains that he intends to stop the Mutant. He shows two kids who were transformed by the Green Beam Machine, and then he gives the player his "word" (the password to enter the path to the top of the building). He sets traps for the oncoming creatures to prevent them from pursuing the player.
In the ending scene, he is celebrating the player's victory with the League of Good Guys.