Skullcruncher was part of the team of Decepticons who participated in an operation to seize the key to the Plasma Energy Chamber from the Autobots. During the battle, the key was briefly used to open the Plasma Energy Chamber, causing it to throw both the key and several Autobots across the galaxy to the planet Nebulos. Skullcruncher and several other Decepticons were then sent to Nebulos to retrieve the key.
In the initial scuffle on the planet, the Decepticons managed to capture several of the Autobots, but the Autobots managed to rescue their allies by becoming binary bonded to a group of Nebulan rebels, turning them into powerful "Headmasters". Skullcruncher and the Decepticons later encountered Nebulos' corrupt ruling council, the Hive, and became binary-bonded with the members of the Hive to combat the Autobot Headmasters. Skullcruncher's head was thus re-engineered to become an exo-suit for the Hive member Grax.
The Decepticon Headmasters then launched an attack the Autobots to retrieve the key. After stealing it from the Autobot Brainstorm, the Decepticon Headmasters all returned to Cybertron with their new Hive allies to help Galvatron fight off the Autobots on the planet. After pushing back the Autobot forces, Galvatron used the key to open the chamber, planning to use it to destroy Cybertron and Earth. After Galvatron's plan was foiled, Skullcruncher and the Decepticons escaped aboard Scorponok, only for a plasma energy shot to knock them into the depths of space.
Transformers: The Headmaster
Four million years ago, Skullcruncher was among a group of Cybertronians who left Cybertron under the leadership of Fortress to escape the eternal war that had consumed the planet. After crash landing on the planet Master, the Cybertronians made several technological quantum leaps to survive in the planet's inhospitable atmosphere and rapidly-changing environments, including the creation of larger, lifeless Transformer bodies called transtectors that would allow them to become "Headmasters". However, Skullcruncher and several others ended up rebelling against Fortress and siding with a traitor named Scorponok.
The traitorous Headmasters later pledged their allegiance to the Decepticon leader Galvatron and joined the Decepticons to assist them in defeating the Autobots.
After the death of Scorponok, Skullcruncher and the other Decepticon Headmasters were forced to flee Earth.