History in Halo: Combat Evolved
 First Encounter
After the Pillar of Autumn crashed into Installation 04, the Master Chief along side with Cortana started to search for survivors. After finding most of the marines, Cortana detected a signal of Captain Jacob Keyes from the Covenants' Truth and Reconciliation Cruiser. After arriving at the location that the Cruiser is stationary, the Master Chief went to the Cruiser in search of Keyes. After taking out Orna 'Fulsamee, and rescuing the Captain, the Master Chief left the Cruiser.
 The Flood and Rescuing Keyes
An important point to make is that the Covenant Cruiser featured in the level Keyes is not the Truth and Reconciliation. It is an entirely different cruiser altogether. People often assume that the Chief has to return to the same Cruiser to rescue the Captain twice. This is not the case. At the beginning of the game, Captain Keyes is kept in captivity aboard the Truth and Reconciliation after being taken captive from the Pillar of Autumn (Human Starship) in the events of the opening of Halo. Master Chief and a team of Marines then assault the Cruiser to rescue the captain.
After the Flood outbreak on the level 343 Guilty Spark and his ensuing capture, as well as the events in Two Betrayals, Cortana and the Master Chief decide that the task falls to them to rescue Captain Keyes and use his neural implant to destroy the Pillar of Autumn, which will cause an explosion that will destroy Halo, rendering it useless as a beacon that could be used to set off a chain reaction that would destroy the universe. Unfortunately, when the Chief and Cortana locate The Captain aboard the distressed Covenant cruiser in Keyes, he has already been assimilated by the Flood and turned into a Proto-Gravemind.