Other variations in gameplay occur over the course of the game as well, such as a competitive bungee-jumping and fighting level, and an underwater maze that must be traversed both within a timelimit and without crashing too many times. If the player loses, a boss fight against Psy-Crow must be won in order to progress to the next level. If the player wins, the next level is started instantly.

The player must direct Jim on his rocket, in a race against Psy-Crow, through a tube-like structure while collecting items and boosts and avoiding asteroids. Unlike the rest of the game, it places the viewpoint behind Jim. In-between most levels, a racing level called 'Andy Asteroids' is played.

Two villains made their only appearance in this game, Chuck, a junkyard man with a tendency to vomit bizarre objects, and Doc Duodenum, a crazed organ of a giant alien. The game incorporates a large variety of villains in the boss battles, including Hickboy, Psy-Crow, Queen Slug-for-a-Butt, Evil the Cat, Bob the Killer Goldfish, Major Mucus and Professor Monkey-For-A-Head exclusive Robotic Chicken. Levels commonly culminate with a boss battle. Failure to do so results in Peter lashing out at Jim, taking away from his health. For example, the level 'For Pete's Sake', involves making sure the computer-controlled Peter Puppy character gets through the level unharmed, which is accomplished by whipping him to make him jump over pits, and defeating enemies before they can damage him. Some levels have additional requirements beyond merely getting to the end of the level. The whip move also allows the player to grab hold of, and swing from, certain hooks in the game. The player can use Jim's gun as a method of shooting enemies, or his worm body as a whip for whipping enemies. The player controls Jim and must maneuver him through the level while avoiding obstacles and enemies.

The game plays as a 2D sidescrolling platformer with elements of a run and gun game as well. Jim in the 'New Junk City' level on the Super NES version

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