Watch the cutscene in the middle of Reclaimer and the Terminals, bro. Everything's explained pretty clearly. The Ur-Didact took the Composer and committed crimes against the Mantle by using it on the Librarian's humans on Omega Halo, she pursues him and incapacitates him aboard his ship with a Binary Rifle. She then seals him away inside his Cryptum in Requiem so his mind can recover through many years of meditation on his choices so that when he awakens he will find a newly evolved humanity and he will help them attain the Mantle. However, Ur-Didact's experience in a Flood-infested system and torture at the hands of the Gravemind drove him into insanity, and the Domain which was supposed to heal his mind in the Cryptum was destroyed when the Halos fired, as the Precursors reveal that the Domain, Mantle and Organon (a Forerunner myth) are the same and based off the Precursors' neural physics which the Halos destroy. Ur-Didact is left to stew in his hatred and Flood-addled insanity for 100,000 years. He awakens rather grumpily when he sees that humanity, the enemy he fought against and the cause of the death of all his children, has endured and are taking what he believes belongs to the Forerunners alone.