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After Optimus Prime and his troops aboard the Ark went missing, Brainstorm was one of several under the leadership of Fortress Maximus. Their faction was mired in a seemingly endless war with a band of Decepticons led by Scorponok, in a struggle so pointless and self-perpetuating that Fortress Maximus decided to leave Cybertron and its war and settle on the peaceful planet Nebulos. Brainstorm followed Fortress Maximus's lead, building the Steelhaven and departing their war-torn home.
It would not be so easy. The Nebulans were xenophobic towards the strange robots which invaded their world, and after several missteps in communication, Fortress Maximus, Brainstorm, and a handful of others surrendered their heads as hopeful proof of their benevolence and compliance.
When the Decepticons arrived on Nebulos, Fortress Maximus and Brainstorm convinced Galen to attempt the creation of hybrid warriors through a bio-mechanical engineering process. An experimental surgeon named Arcana constructed the necessary equipment based on the Autobots' theories and underwent the process himself along with several other Nebulans, binary bonding with Brainstorm.
During an adventure that happened at some unspecified point that was logically impossible given the circumstances, Brainstorm and the other Autobot Headmasters fought the Decepticon Headmasters while the Autobot Targetmasters were held captive by the Decepticons. Mindwipe hypnotized Brainstorm, causing him to crash into Hardhead, and in general, the Autobots put up a terrible fight. But Brainstorm refused to give up and abandon their captured comrades. The four attacked the Decepticons' Fortress of Despair and were overwhelmed, but because the Autobots learned to work together with their new Nebulan partners, they were able to rescue the Targetmasters.
The new Headmasters managed to drive off the Decepticons, but also inadvertently created a new "arms race", as the Decepticons later created Headmasters of their own, and both sides also implemented Targetmaster warriors as well. Fearing things could only get worse for Nebulos, Fortress Maximus and Galen took the excuse of an intercepted distress signal from Earth to abandon Nebulos and prevent the war from causing any further harm to the planet.
On the way to Earth, Brainstorm re-engineered Fortress Maximus to be larger and stronger than ever before. Then, he and Arcana managed to triangulate the Autobot signal to Mount St. Hilary. This led into their first battle with Scorponok's forces on Earth and to the death of Galen.
As the Steelhaven orbited the Earth, Brainstorm was kept busy building Goldbug a new body, repairing the injured Fortress Maximus and assisting in the creation of the Autobot Pretenders. Unfortunately, those projects used up most of the group's available resources and prevented the proper recreation of Optimus Prime. The project proceeded despite Brainstorm's accurate warnings of failure.Brainstorm was displaced to Limbo along with a handful of other Autobots when Rodimus Prime traveled to the past with a group of Autobots of his own.
Later, he was one of the victims of a rogue Autobot Mark V Guardian droid, which resulted in him being thrown from the Ark and landing at the feet of Optimus Prime. Brainstorm's flaming body helped contribute to the Autobot leader regaining his desire to fight.
Brainstorm was killed when Unicron ravaged Cybertron in 1991. Even Brainstorm's vast intellect failed him when confronted with the devil himself, so he simply screamed and shot desperately until Unicron scooped him up. He was quite tasty.
- His character model in the Marvel UK comics is the most accurate to the toy having both a faceplate and a teal color-scheme.
- In early planning stages, the Large Headmasters were to have differently styled heads that would be replaced by their more familiar heads during the Headmaster process. A commercial for Headmasters #1 featuring animation of Brainstorm and others is the only time these designs were used.
- Additional footage of the Headmasters featured in the animated introduction to the first commercial for the Pretenders. As Brainstorm battles Mindwipe, the narration claims that after a series of defeats, the Autobots are required to up the ante by developing Pretender technology.