In the game, Takato Matsuki and Guilmon find that Henry Wong and Rika Nonaka have had their Digimon kidnapped to serve the Master. The two discover through Impmon that the source of the disturbance is at the Sewers, but hordes of Digimon guard the place, so they have to assemble the secret device. Fighting through the RedVeggiemon at the Docks, Dokugumon at the Junkyard and Etemon at the Amusement Park, to obtain the needed parts, Takato and Guilmon combine them, only to have Impmon try to convince Guilmon to abandon Takato. Guilmon refuses, and the two head to the Sewers to rescue Calumon. Using the secret device to make themselves invisible to the Digimon army, they defeat SkullMeramon to save Calumon. Calumon tells them that they need to seal the portal used by the Master to allow Digimon to enter the Real world using the portal key. After defeating MetalSeadramon at the Docks, with side trips to the Junkyard and Amusement Park to rescue the brainwashed Gargomon and Kyubimon, Takato and Guilmon seal the portal only to find the Master: Myotismon. Defeating him, Takato and Guilmon save the world.
Players use the keyboard arrow keys to control Takato on the overworld. There are four locations: Docks, Amusement Park, Junkyard, and Sewers. The first three places consist of several screens, each of which may contain an enemy, as well as a minigame area, where to cross Takato needs to either solve a puzzle or dodge objects. The Docks require Takato to cross an open space of water on the backs of several rows of dolphins moving in alternating directions. The Amusement Park is a slider puzzle made up of bumper cars, where the cars only move certain spaces in certain directions. The Junkyard contains a Frogger-style crossing game where Takato has to avoid being hit by bulldozers as he crosses.
When an enemy attacks, Guilmon steps to the fore. Battles are one-on-one, where each side inputs commands at the beginning of the round and then attack based on speed. By equipping DigiCards, Guilmon can use various techniques to dispatch his enemies, though he can only use three at a time, not including the Flee command. He can switch Cards at any time in the battle.
There are three types of attacks, Physical, Energy, and Support; the first two have their own separate defenses, while the third supports the user.
Guilmon has three slots to use; each DigiCard uses a one, two, or three slots depending on its speed, with the faster the technique, the less slots it takes. Once ready, Takato gives the command, and Guilmon attacks. If Guilmon loses, Takato is returned to the start of the screen. If he wins, they reap rewards, usually consisting of EXP and, in some cases, DigiCards. With more EXP, Guilmon can increase in level for more stats. At level 7, he digivolves to Growlmon and remains that way.
If Takato gets through the Sewers before completing the secret device, either via brute force or by sneaking around the vast number of enemies carefully, he will find the Omega Blast DigiCard. This is the only way to acquire this DigiCard.
If the secret password "guilmon" is entered in the text field on the title screen, Guilmon and Growlmon will have double maximum health for the duration of the game.