Season 1

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

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.

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

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.

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.

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.

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.

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.

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 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.

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.