The Penal Zone
General Skun-ka'pe appears in the first part, destroying parts of New York City with the intent of conquering the planet. Sam and Max, using various Toys of Power that work with Max's psychic abilities, manage to activate the homing beacon on Skun-ka'pe. With more effort, they manage to reimprison the intergalatic criminal into the Penal Zone, an alternate dimension designed to keep beings like him from causing harm.
Unfortunately, this is all only a vision of the possible future seen through one of the Toys. Skun-ka'pe arrives on Earth under the pretense of only seeking fair trade. His real intentions of finding the Toys of Power are revealed but he too has seen the aforementioned vision. With this knowledge, he steals the Toys in Max's possession and has the duo imprisoned in the Penal Zone. However, Max's teleportation abilities allow them to escape.
With the aid of a "dimensional destabilizer", the duo trap Skun-ka'pe but are unable to get him recaptured into the Penal Zone due to the simian's strength. Max then tricks Skun-ka'pe into letting go by convincing him that an ordinary paddleball is another of the toys sought out. Skun-ka'pe is then imprisoned in the Penal Zone once more.
They Stole Max's Brain!
In the third segment, Anton Papierwaite (the main antagonist of the previous segment) steals the Devil's Toybox (which would house the Toys of Power) offscreen, an act that frees Skun-ka'pe from the Penal Zone. Seeking revenge and a way to claim the Toys for himself, Skun-ka'pe literally steals Max's brain to function as a summoner. He and Papierwaite briefly battle over control of the Toys until Sam appears to rescue Max. Recognizing Sam as a common enemy, Skun-ka'pe forms an alliance with Papierwaite and channels their collective abilities (his technology with Paiperwaite's magic in conjunction with Max's psychic powers).
Their plot is sidetracked when Sam inserts the brain of a former child pharaoh Sammun-Mak into Max's body for temporary assistance. Sammun-Mak seizes control of the Devil's Toybox and warps reality to his favor as supreme overlord. In this reality, Skun-ka'pe is Sammun-Mak's champion gladiator, beating and killing opponents in a ring for the demented pharaoh's amusement. However, Max's brain manages to direct a warped Sam (as Max is the only character not warped to worship Sammun-Mak) to defeat Skun-ka'pe by goading the simian to insult Papierwaite who attacks Skun-ka'pe with magic. Thrown off-guard, Sam defeats Skun-ka'pe. The simian vanishes after reality is restored following Sammun-Mak's defeat.
The City That Dares Not Sleep
After nearly being taken out by Sam's numerous clones brought into being by Charlie Ho-Tep, Skun-ka'pe returns to continue his collection of the Toys of Power. Although most of them are destroyed following Charlie Ho-Tep's defeat and destruction, the toy robot-like Cthonic Destroyer (which can destroy anything from the Dark Dimension the Toys originated from) is still about. Needing it to hopefully cure Max of his demonic Godzilla-like state, Sam seeks the Cthonic Destroyer. However, it is in Skun-ka'pe's possession.
Using the other surviving Toy the Astral Projector (which permits the user to project their consciousness into a similar being's body), Sam directs one of his surviving clones to seek out Skun-ka'pe. With a fog machine and image projector, Sam tricks Skun-ka'pe into giving the Cthonic Destroyer under the threat of destroying the nonexistent Devil's Toybox. Beaten, Skun-ka'pe retreats in his spaceship. Unfortunately for him, the demonic Max, embedded with a warhead and wanting to save the Earth, teleports aboard Skun-ka'pe's ship. The resulting explosion kills the ship's inhabitants.