After the universe ends, the Super Eon Annihilator’s consciousness awakens. He is spoken to by the Vanishing Commutator.
He is informed that his ability to travel through time (and send others through time) was granted so that he would gradually fracture reality. This fracturing ensured that when the universe ended at the hands of Chaos, that rather than a new universe coming into existence, a new multiverse would come to be.
The Vanishing Commutator had also planned to give the Super Eon Annihilator his knowledge and abilities if Chaos were ever freed, freeing him so that he could end his own existence to stop Chaos’s dominion from extending beyond the end of the previous universe.
With the Vanishing Commutator’s knowledge and power, the Super Eon Annihilator begins to teach himself how to create and manipulate universes. He learns to restore life, bringing back his friends and those that helped him try to save the previous universe; this was made possible because their consciousnesses were transferred to the Super Eon Annihilator by the Vanishing Commutator before he ended his own existence.