The pirate captain Longhorn Silver and his band of buccaneers have been robbing trains and causing trouble on Moo Mesa's waterways. With a gold shipment and Cody's money for new boots in their possession, Moo Montana, Dakota Dude, and Cowlorado Kid have to go to Newportleans to track these pirates down. While trying to get back the money, Cody is caught by the Masked Bull as part of his plan to work with Longhorn Silver to dispose of the C.O.W.-Boys. Now the C.O.W.-Boys must rescue Cody, reclaim the stolen loot, and defeat Longhorn Silver.

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.

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.

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.