He decided to forsake the Time Lord's agreement to not meddle with history and decided to alter the history of planets for his own selfish and devious ends. He manipulated the cultures of many soon-to-be space faring worlds so that their earliest ancestors worshipped him, and soon he had risen an army of followers.
At some point he joined the Pantheon of Dischord, and was a close ally of Tricky Tricky. During his time with the Pantheon he destroyed several Dalek fleets as well as hunting down and murdering the three Time Lords that issued his outcastment from Gallifrey, before they had even done so. This made him a paradox and therefore erased him from history, reversing his meddling with time and resurrecting his condemers. However, he himself survived in some form.
It is assumed that he perished during the Time War, but since his resurrection he can no longer be officially classed as a Time Lord anyway, so even if he survived, he would be of no help to the true Last of the Time Lords, his old friend the Doctor.