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.

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.

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.