-Vladin RasKilmer: The first villain that the Trouble Shooters face off against. He's a notorious Russian crimelord and plans to plunder the city of Ecto Valley.
-The Dalton gang: These guys first appeared in The Good The Bad and the Huckleberry Hound. In Trouble Shooters, they appear as a bunch of big time wanted Criminals. They rob banks, cause chaos, steal, and the like. Plus, they're not too bright. The members as follow:
Dinky-He's the biggest of the bunch, and he's not too bright.
Pinky-He's a real ladies man. He dresses in pink clothing (not to be confused with dresses). His main catchphrase is calling people 'Rotten Dresser.'
Finky- He's the whiniest of the bunch and the smallest.
Stinky-He's small, but bigger than Finky. He's considered the leader.
Hungry- He packs up quite an appetite, literally. His personality is based off of Berger Beagle of the Beagle Boys.
Carny-He's really a cousin of the Daltons, yet retains the Dalton name. He resides in Columbia, and loves the thrill of crime, and loves the sound of gunfire. His personality is based off Don Karnage from Talespin.
Brainy Dalton-The only Dalton brother whose the smartest in the family. Although inspired by Megabyte Beagle, he's very much similar to Brain [Pinky and the Brain]. XD
-Dr. Animalector: the most sneakily and creepiest doctor the TS’ ever faces. He’s known to cheer on the heroes, and somewhat intimidate them at the same time. Dr. A is an animal psychologist, studying each animal’s behavior. He’s also known to perform all sorts of evil experiments on animals.
-Randall J. Swiper: the richest kid in Ecto Valley; his goal is to become the richest kid in the world. He’s also Christopher Peeper’s rival. He’s always cooking up schemes and is always trying to stop Chris from getting the better of him.
-Dr. Von Time: A mad scientist whose obsessed with time and technology. At some point in the series, he creates a brand of cyborgs called Timeanators. More details to be revealed about him soon.
-Chris P. Bacon: Not to be confused with our hero, Christopher Peeper; Chris P. Bison is a very powerful space dictator in the video game universe. His appearance is basically a pig dressed up in M. Bison's clothing. And his sidekick is Kernel Flanders. They're both very comical villains. How the Trouble Shooters meet them, is a secret.
-Anti-Chris—the doppelganger of Christopher Peeper. He longs to dispose of the real Christopher Peeper so that he may be free to do whatever he pleases. Appose to Christopher, he dresses in yellow jacket and pants, and a red shirt. And he has a very deep voice.
-Hands Grabber—clever, slick, and never likes to be disappointed. He’s the leader of an international terrorist group. Like any other villain, he desires power. His appearance is very similar to Moses from Superbook season 2, due to the likeness of Shere Khan He's accompanied by his henchman named Earl, Bert, Ernie, Max, etc.
-Dick Dastardly and Muttley—the infamous duo from Wacky Races. They’re known to be ‘double dealing do-badders.’ However, their dastardly deeds aren’t as threatening as any other villain put together. They're more of a semi-regular on the show.