Agent Vess comes to Empire City following a series of crimes and is severely injured by the Big Boss and his Henchmen.

Big Boss plans to rob a large group of guests on-board Empire City's premier blimp.

Dr. Badvibes is using the cover of a circus to rob the banks of Empire City.

A mysterious figure known as the Bugman is committing a series of heists in Empire City.

Berserko plans to throw a surprise party for Big Boss.

The C.O.P.S. are endangered of being replaced by a new brand of crime fighting robots known as The Instant Justice Machines, which proves to be much better in handling law enforcement than the C.O.P.S....sort of. The C.O.P.S., however, has smelled a rat. And his name is Head Councilman, Vargas, who is bribed by Big Boss to continue to make the robots and put C.O.P.S. out of business in a most corruptive way. Can the C.O.P.S. team stop Vargas and put an end to his own brand of justice for good?

Rock Krusher has taken over Graystone Prison and plans on using a large device known as The Neutron Pulverizer to disintegrate City Hall unless demands are met by 6:00 pm. Bowser, going undercover as a prison inmate named "Maddog", was able to radio the C.O.P.S. team on Krusher's plan just before Krusher cuts off all communications to the outside. The only way for the C.O.P.S. team to stop Krusher's plan is to break into the prison the same way inmates break out.

Johnny Uma , the ex-partner of Sundown, escapes from prison and plans a heist on the Silver Bullet Train.

C.O.P.S must unite to fight Big Boss and his ultimate crime machine.

Dr. Badvibes has designed a series of speed suits that will make Big Boss's criminals difficult to catch by the C.O.P.S team.

The Big Boss wants to have Bulletproof replaced with a fake copy that he can control.

Dr. BadVibes created a dog whistle-like device and used it on Blitz, forcing him to ruin the efforts of the C.O.P.S. team to perform their duties. Both Bowser and Mainframe must find out what or who's causing Blitz's off-the-wall behavior and must also rescue Dr. Gregory Adams, too, who was force by Berserko to tell the C.O.P.S. team that Blitz must be decommissioned because of a glitch found inside him, while in fact there's nothing wrong with him.

A small midget-size man known as The Baby Badguy and his 2 henchmen poses as orphaned babies to get into the newly opened Empire City Orphanage to take over the place and used it as their hideout. They took hostage the caretaker of the orphanage and Whitney Morgan, who came to interview the caretaker. The C.O.P.S. team must rescue the hostages and discipline those three naughty "babies".

Dr. BadVibes decides to toy around with the idea of creating toy size robots and programmed them to steal items from the homes of the children who own them. Brian O'Malley gets one of the robots for his birthday. Named "Rocky", this robot went and stole a family heirloom, a leprechaun statue passed down from LongArm's great-grandfather and ran off with it. Brian followed the robot to where Badvibes set up his hideout at an old abandoned toy factory right near the sewers. There, he was captured and is held captive by BadVibes, who wound up arguing with Buzzbomb over the share of the stolen loot, hurting his feelings in the process. Brian must talk Buzzbomb into releasing and helping him, Sundown, and his father put a stop to BadVibes and his army of thieving robots.

Mayor Davis is enraged when his Limousine gets stolen by Nightshade and Squeeky Kleen who are planning on converting it into Big Boss' own personal limousine look-a-like along with all of the other cars they stole. He demands Highway and Hardtop to get his limousine back....or else! Meanwhile, Highway must go out and get his Bluestreak motorcycle back that was stolen from Nightshade before it shares the same fate as the other vehicles she stole.

Big Boss stage a special Crooks Convention in Empire City where he plans on giving out The Criminal of The Year Award to one lucky crook. Buttons McBoomBoom and Berserko both duke it out to see who will have that title.

The cops have to face a shapes changer robot, who's stealing all around the city.

Dr. BadVibes created an earthquake device known as The Ground Shaker for Big Boss who plans on using this device to level the city to the ground unless his demands for the city are met. It's up to the C.O.P.S. team to stabilized the city and shakedown Big Boss' crooked caper.

Mainframe, Bowser, and Blitz pays a visit to a large newly opened shopping mall to foil Dr. BadVibes plans to steal a super computer brain to the mall's theft proof security system created by Mr. Keen, the head of mall security.

Three of the best Boxoids (robot boxing suits) have been stolen by Big Boss who plans on using them to steal the mazer melter from a construction site and use it to melt down the Empire City Power plant and cause a major blackout over the entire city unless Mayor Davis can cough up twenty million dollars in one hour. It's up to the C.O.P.S. team to K.O. Big Boss' plans before it's too late.

In this caper, C.O.P.S. are aided by a very unusual ally - Cindy Johnson as Captain Crimefighter! A little girl in a superhero costume who helps the team capture Rock Krusher, Turbo Tu-Tone, and Ms. Demeanor and, along the way, uncover 2 bags of stolen cash hidden at a construction site taken from a robbed bank by Krusher and Turbo.

Berserko stole a special headband that made him very unusually intelligent when he puts it on his head. In this new form, Berserko makes plans to intelligently trap the C.O.P.S. team at his amusement park hideaway while inciting Dr. BadVibes' jealousy of his new-found brilliance.

Mickey O'Malley, LongArm's father gets arrested for a crime he didn't commit. He was falsely accused of stealing priceless furs from a warehouse and is sent to prison for it. It's up to his son and his grandson Brian to help clear his name and send the real crooks responsible for the fur heist to the slammer.

The city's criminals made a spa with device that controls brains, and their first client in the grand opening is the governor.

Brian befriends a prehistoric caveman who was frozen in ice since the Ice Age. This spark interest from the Crooks since the caveman bears a striking resemblance to Berserko and is believed by the crooks to be Berserko's direct ancestor.