In the introductory scene, under orders from the villainous Mollusc, Ghosts Inky and Clyde steal a magical power pellet known as the Artifact that has kept Pac-Land free from evil. The Mollusc smashes the Artifact and in a mighty explosion of power, its four fragmented pieces are scattered across time and space. The player's challenge as Pac-Man is to retrieve the Artifact's four pieces from the now ghost-infested time periods and return them to the present. Professor Pac-Man prepares an unpredictable, hastily constructed Time Machine to help Pac-Man on his quest.

Pac-Man initially travels through four different time-periods, including prehistoric times, Ancient Egypt, the Middle Ages, and the Wild West. Although the Time Machine sometimes malfunctions, sending Pac-Man to an unexpected place and time, he is eventually able to obtain in each era one of the four pieces of the Artifact. Afterwards, the Time Machine malfunctions again before Pac-Man can return to the present, instead bringing him to a fifth time-period: the future. Professor Pac-Man claims that an alternate power source is needed to bring him home from the future. In this fifth time-period, Pac-Man finally comes to the Reactor Core and is able to harness its energy to be finally transported, with the Artifact reassembled, to the second after the Mollusc broke the Artifact in the game's introduction scene. Aiming the now-repaired Artifact at the Mollusc, Pac-Man fires a beam of light at his foe, vaporizing the Mollusc and grinning triumphantly.