The game consists of a series of missions with varying gameplay styles, for instance, throwing donuts at criminals a la target practice or navigating a maze looking for pieces of clothes to identify a criminal based on a sketch.
Bonkers notices a "Officer of the Month" competition and decides to enter and win it to make Lucky proud of him when he returns from vacation. To do so, he needs to capture four wanted Toon criminals: Harry the Handbag, The Rat, Mr. Big, and Ma Tow Truck.
Each of the four Toon criminals that Bonkers needs to arrest to win the "Officer of the Month" competition has a different gameplay aesthetic to it:
- Harry the Handbag and his gang of raccoon thieves are trying to steal five treasured artifacts from the Toon Museum:
- Bonkers needs to smack a pre-set number of Harry's raccoons with doughnuts to stop them. The raccoons can sometimes throw their own doughnuts back at Bonkers, and later stages have Bonkers dealing with bats that try to swoop down at him and if Bonkers hits the bust of the Mad Hatter too many times, it will come to life and attempt to attack him for a short period before returning to its pedestal until disturbed again. Every three rounds, Bonkers plays a bonus round where he has to navigate several pillars in the air to reach Harry. If he is successful, he wins an extra life, or if Harry's raccoons successfully stole one of the artifacts, Bonkers will get it back for the next three rounds. Bonkers loses a life if he either loses all 5 of his hearts in his health bar or the raccoons make off with all five artifacts.
- The Rat is hiding out in the local junkyard where the Junk Machine is causing all sorts of trouble spewing various trash everywhere, so Bonkers needs to build a wall to stop it. However, the Rat will come along and smack some of the bricks out with his mallet to delay Bonkers from completing the wall and leave him at the mercy of the Junk Machine. Like with Harry, every three rounds allows Bonkers to perform a bonus round with jumping from various platforms to reach an extra life. Bonkers can occasionally collect a special brick that, if thrown and it hits the Junk Machine, will temporarily incapacitate it for a few seconds so Bonkers can focus on the wall without dodging all manner of trash like bowling balls, trash can lid frisbees, exploding soda cans, windup Toon chattering teeth, parachuting dynamite, bouncing springs, Toon pogo sticks and tires, and more. Bonkers loses a life if the Junk Machine's garbage takes out all 5 of his hearts in his health bar.
- Mr. Big is hiding in the Toon Warehouse with the intent to blow it up with a large Toon bomb. Bonkers' buddy Fall-Apart Rabbit can help defuse the bomb, but he's fallen to pieces again, so Bonkers needs to locate the containers that Fall-Apart has his pieces in to reassemble him, but Mr. Big's henchmen will try and stop Bonkers by making him drop pieces of Fall-Apart that will disappear and be placed in another container if Bonkers doesn't recover them in time. Bonkers needs to find all eight pieces of Fall-Apart before the bomb's timer runs out, or he loses a life. He also loses one if Mr. Big's henchmen take out his health bar. The bonus round is the old shuffling cups trick where Bonkers needs to watch carefully for where the box containing Mr. Big starts and where it stops after the boxes are shuffled around. If he finds the right one, he gets an extra life.
- Ma Tow Truck is causing havoc on the freeways with her gang of criminal cars. Bonkers needs to take his own patrol car out onto the freeways and try to stop them using any means possible, including bumping them off the road, spinning them out with oil slicks, or sticking them to one spot with bubble gum. The Toon Helicopter will assist him by airdropping ammo, health, and a shield at regular intervals. Bonkers has to eliminate a set number of the henchmen before Ma will show herself personally, where Bonkers needs to whittle down her health bar to zero to complete the current round. Later rounds have Ma step up defending herself with hauling one of her henchmen behind her to use as a trap for Bonkers, releasing it to blow up in his face, or potholes that force Bonkers to slow down to avoid taking damage from driving over them. The bonus round has Bonkers keep up with the Toon Helicopter as it drops hearts for him to collect. If he collects all of them and does not miss so much as one, he wins an extra life. If he loses all 5 of his health bar's hearts while pursuing Ma and her cronies, he loses a life, with the scene that plays when it happens showing Bonkers' pet Toots playing the Funeral March before changing to Shave and a Haircut for comedic effect.