Galvatron succeeded in taking the Matrix from Ultra Magnus, but instead of destroying it, he used it to blackmail Unicron. However, he was unable to open the Matrix, and Unicron swallowed him as punishment.
Unicron transformed into his humanoid mode and physically attacked Cybertron. Apparently led by Shockwave, the Decepticon troops occupying the planet fought back, but with little effect. The Autobots, using a Quintesson cruiser and a Junkion starship, joined the battle. The Dinobots were able to cause some damage to Unicron's posterior, but did nothing serious. The Junkion ship was able to withstand some sort of flame that was fired from Unicron's mouth, but was ultimately destroyed when Unicron caught it in his hand and crushed it. Badly damaged, the Quintesson ship collided into Unicron's eye, destroying it and causing the ship to fall apart.
Hot Rod fell out of the disintegrating ship and ended up coincidentally in the same region as Galvatron. Galvatron proposed an alliance between the two, but Unicron wracked his body in terrible pain until he agreed to destroy Hot Rod. Hot Rod gained possession of the Matrix and used it to become Rodimus Prime. When Galvatron shot the Matrix out of his hand, Rodimus threw him through Unicron's exoskeleton and out into space. He then regained the Matrix and used it to annihilate Unicron from within. Rodimus then found the other Autobots inside and led them out through Unicron's remaining eye, destroying that also. The only part that remained intact following the explosion that engulfed Unicron was his head.
In 2005, Cyclonus led a group of Decepticons into Unicron's head to
try and locate the whereabouts of Galvatron. They were successful in activating
and using Unicron's computer, and though Cyclonus reassured Scourge that
he was dead, Scourge was unconvinced. Scourge turned out to be correct,
and though Unicron was now relatively powerless, he was indeed still alive.
In a deal with the ghost of Starscream, Unicron recreated his body in return
for help in regaining his eyesight and obtaining Cybertron for his new
body. Starscream did get the eyes by stealing them from Metroplex and Trypticon,
but Unicron was unable to get Cybertron.