From Halopedia, the Halo wiki
Walkthrough: During the level Midnight, shortly after boarding the Mantle's Approach. Get to the third room with enemies in it. There should be no Knights here. The Terminal is located in this room's central structure.
The Mantle's Approach flies through a nebula. On the bridge, the Didact, lacking his outer armor, is steering the ship as the Librarian appears behind him, wielding a Binary rifle. The Didact turns around to face her.
The Librarian fires a shot at the Didact's chest and he falls on a knee. He looks at the Librarian, who hesitates for a moment, then fires another shot. The Didact falls on the deck, motionless.
Cut to one of Requiem's access portals, then a series of spires inside the shield world.
The Librarian observes as the spires retract into the bowels of Requiem, then floats away along a hallway.
The Librarian enters a room where the still-unconscious Didact lies. Caught in an anti-gravity field, his body begins to rise from the floor.
The Librarian observes as a series of pillars descend around the platform housing the Didact's Cryptum.
The Librarian calmly puts her hands around the head of one of the Knights, and its orange lighting turns blue.
A small platform transports the unconscious Didact into his Cryptum.
The Librarian floats away amidst the rows of now blue-lit Promethean Knights. Cut to a view outside Requiem as the shield world's access portals seal off.