The behavior of the Ur-Didact following his encounter with a Gravemind and return to the Forerunner civilization became more erratic and harder for the IsoDidact and Librarian to cope with as the Forerunner-Flood War continued. When the Ur-Didact refused to participate in the defense of the Greater Ark and instead used a Composer to consume the essences of many humans living on Omega Halo against the will of the Librarian, his actions were deemed untenable and had to be dealt with. During the Battle of the Greater Ark, the Ur-Didact left for Requiem, and the Librarian followed close behind in order to put a stop to what were considered actions of a madman. Upon arrival on Requiem, the Librarian incapacitated the Ur-Didact, placing him within his own cryptum on the planet, leaving him to rest and meditate until the galaxy repopulated itself.
Though unknown to the Librarian at the time, the Domain, which the Librarian hoped the Ur-Didact would access and use during his time in the cryptum, was severely damaged by the Halo Array, and the Didact spent the next one-hundred thousand years alone with only his thoughts.