Cow Belle and her sons have an underground hideout called Sidewinder City which allows other outlaws to use it in exchange of a share of what they steal. When Cowlorado Kid is captured during the infiltration, Moo Montana and Dakota Dude must find Sidewinder City and rescue him while also dealing with the Masked Bull.

Cowlorado volunteers for Miss Lily's cattle drive only to find out his "cattle" is actually a bad tempered sheep named Miss Ewebaby. Moo and Dakota discovery that the cattle drive is a front to delivery the money for the Elbow's Bend Hospital Veterinary Clinic where it is under Miss Ewebaby to keep it from being stolen by The Masked Bull.

Mayor Bulloney and The Masked Bull make a plan to get rid of Moo Montana with literally explosive results.

Moo Montana and Sheriff Terrorbull get in a mess when they both try to capture the Gila Hooligans after the crashed the party in Cowtown that followed Mayor Bulloney's re-election. To catch the Gila Hooligans, the C.O.W.-Boys and Sheriff Terrorbull have to work together to apprehend the Gilla Hooligans.

The Great Bovini's Wild West Circus comes to Cowtown, but amusement of the masses is the last thing on the mind of the ringmaster The Great Bovini as he uses a special stone to mesmerize anyone into stealing money. In order to keep the Cowinoor Diamond from being shipped to the Jersey City Museum, Mayor Bulloney, Saddle Sore, and Boot Hill Buzzard approach The Great Bovini to help them steal it which doesn't go well as Boot Hill Buzzard is unaffected by The Great Bovini's stone. Now the C.O.W.-Boys must work with Boot Hill Buzzard into thwarting The Great Bovini and freeing the townspeople from his control.

On Halloween, Skull Duggery returns upon emerging from the cave-in of his mine at Skull Mountain in order to get revenge on Moo, Dakota, and Cowlorado. This time, he has obtained an age accelerating spell with the help of his fellow ghosts where they start aging everything in Cowtown.

When Cowlamity Kate doesn't receive a letter from her father who has been exploring the Mesa for 7 years, Mayor Bulloney claims he will be taking all her property since her father had no will. But when a page of one of her father's old letters shows up, stating Kate will inherit the ranch and his gold, though only if she is married, Kate plans to make Dakota her husband.

Cowtown dries up and only Mayor Bulloney has water. When Cody finds the real reason for this, it is up to him to bring water back to everyone.

Moo Montana, Dakota Dude, and Cowlorado Kid apprehend the Cacklin Kid after he was nearly disposed of by the Baying Bunch led by Scavenger who are seeking the location of where the Cacklin Kid hid the Baying Bunch's loot. At the courthouse, Cacklin Kid gets sympathy from Judge Overrule who instructs that Moo Montana, Dakota Dude, and Cowlorado Kid to safely transports Cacklin Kid to the federal penitentiary to serve out his one year sentence. Now the C.O.W.-Boys must get the Cacklin Kid to the penitentiary safely while evading the Baying Bunch who have tricked Sheriff Terrorbull into helping them.

In preparation for the 11th Annual Cowtown Cross Country Race, Cowlorado Kid encounters some competition Cowlamity Kate's cousin Cowleen and her horse Tornado as well as encountering his old rival Swifty Buckhorn. Fast Willy and his henchmen plan to steal Tornado so that they can rob the Pony Express with one of the packages being the trophy for the Cross Country Race. Now Cowlorado Kid and Swifty Buckhorn must put aside their differences to help Moo and Dakota catch Fast Willy and reclaim Tornado.

J.R. takes Cody Calf and Buffalo Bull to the Invention Convention on the Dixie Trixie. Using his airship, Mules Verne and his henchmen steal the Dixie Trixie so that he can force all the inventors onboard to help him take over Moo Mesa by building a giant robot cowboy that will help in his plans by starting with raiding the governor's mansion.

A mysterious bull named Jacques La Beef arrives in town who has all the women drawn to him. Moo and Dakota are suspicious of him, especially after Miss Lily is robbed of the items in her new safe by The Masked Bull in a plot to discredit Jacques La Beef (who is secretly a notorious con artist named Barney Finkleberg).

During an attack on the stagecoach bound for Cow Town, Puma sees that The Masked Bull is actually Sheriff Terrorbull after Boothill Buzzard accidentally unmasks him. In order to save his identity after his attempt on Puma's life is thwarted by J.R., Sheriff Terrorbull must break his younger brother Horribull out of Sinquitten Federal Prison to pose as The Masked Bull and fool everyone.

No one cares that it is Moo Montanta's 10th anniversary as marshal. Then, Moo receives a telegram from Bessy Bluebell from his hometown of Miller Glen where the retiring sheriff T-Bone wants Moo to take over even at the time when Bat Blastagun and his henchmen are causing trouble in Miller Glen. Now Moo must decide between Miller Glen where he is beloved by the townsfolk and Cowtown.

A new teacher (actually Boot Hill Buzzard in drag) has the children help The Masked Bull commit crime through her strange assignments.

Moo Montana, Dakota Dude, and Cowlorado Kid have to deal with four masked marauders who happen to be ladies of the Sewing B. Ranch led by Barb Wire Babs (the criminal alias of Miss Barbara). As Cowlorado Kid goes undercover in Barbed Wire Babs' group, Wild Bill Barker is kidnapped as part of Barbed Wire Babs' plot to make counterfeit money.

When Cody, Carly, and Jake find a treasure map in Cowlamity Kate's attic while cleaning it, they decide to follow it to find Tom Duggery's lost silver on Skull Mountain. While competing against Saddle Sore and Boot Hill Buzzard, Cody, Carly, and Jake encounter Tom Duggery's ghost in the form of Skull Duggery. Now Moo, Dakota, Cowlorado, and Cowlamity Kate must rescue the kids from Skull Duggery.

In an attempt to get his own deputy star, Cowlorado goes undercover as Johnny Slim to catch Five Card Cud all by himself when he and his henchman Short Change take control of the Dixie Trixie river boat while in collaboration with the Dixie Trixie's captain.

The C.O.W.-Boys get word from Warden Gordon Bordon that Billy the Kidder and his lizard henchmen Lester and Kisser have escaped from prison. When Lily's uncle Rocky gets caught in a cave-in upon finding the lost treasure of the Concudsadors, she plans to enlist Cowlamity Kate to help rescue him only to end up captured by Lester and Kisser so that Billy the Kidder can steal the lost treasure of the Concudsadors. Now the C.O.W.-Boys and Calamity Kate must rescue Lily and Rocky, apprehend Billy the Kidder's group, and recover the lost treasure of the Concudsadors.

Bat Blastagun and his gang have escaped from prison where they find a shard of the comet that created Moo Mesa outside of Cowtown. Enlisting the help of the mad scientist Dr. Wolfgang Wolfenstein, Bat Masterson uses the shard to shrink everything.

Cowlorado Kid discovers gold in a river causing the Gold Rush on Moo Mesa which even gets Mayor Bulloney, Saddle Sore, and Boot Hill Buzzard to work on claiming the gold. Upon Boom Town being formed as part of the gold rush, the C.O.W.-Boys work to keep the settlement in line. When a claim-jumper named Big Bucks and his henchmen Digalong and Stub plot to steal everyone's gold, the C.O.W.-Boys spring into action to protect Boom Town.

The C.O.W.-Boys work to catch two snakes that make up the Hole in the Ground Gang after they robbed some bison at Mini Soda Flats. Cody is really excited about going to the Pueblo's annual Cow-Wow with J.R. and Tejua as the threat of the Hole in the Ground Gang could disrupt the whole fiesta. When Moo and the other C.O.W.-Boys run into some trouble trying to catch the gang, Cody and Tejua help to bring them to justice.

When Mayor Bulloney discovers oil that is secretly buried deep beneath Lily Bovine's Tumbleweed Saloon, he quickly dispatches Lily's arch-rival Sadie Wowcow to run her out of town.

After Cowlorado Kid was unable to catch a gold thief, he, Moo Montana, and Dakota Dude look for the thief and end up escorting a wagon train led by Rooster Cogsbull through a valley where a creature called the Cowgoyle (a cattle/gargoyle creature) dwells. To make sure that the C.O.W.-Boys meet their end and the Cowgoyle is blamed for the action, Mayor Bulloney sends Saddle Sore and Boot Hill Buzzard to get the Masked Bull to dispose of them. Following the Cowgoyle's attacks, the C.O.W.-Boys work to catch the Cowgoyle while suspecting that it might be one of the suspicious wagon train travelers.

Many trains have been stolen by Shock Holiday's gang where Shock Holiday is holding them hostage until the Railroad President pays a huge ransom. When Marshall Moo fails at capturing the thief, Sheriff Terrorbull challenges him to see who catches Shock Holiday first and the loser will have to leave Cowtown.