The Fall of Reach, though brief, was of great significance for John. Here he received the MJOLNIR Mark V Powered Assault Armor which improved his strength and reaction time more effectively than his older Mark IV suit. He was also introduced to and partnered with the AI Cortana, who would become a close friend and ally to him. In the first test of their partnership, the two were put through a practically suicidal test in an attempt by Colonel Ackerson to get rid of John. John refused to cheat the test and was determined to win it by Ackerson's rules. Despite nearly being killed, Cortana and John's teamwork had them pass the test in an early show of the incredible partnership the two would come to develop. The majority of the Spartans, led by Fred S-104, went to the planet's surface to protect the Orbital Defense Generators which powered the planet's twenty Orbital Defense Platforms. John, with Linda and James-005, was sent toReach Station Gamma to destroy an unsecured NAV database onboard the UNSC Circumference. If the Covenant obtained the database, they would discover the location of every human world, including Earth; the location of Earth by then was still a closely guarded secret. The NAV database was destroyed, but Linda and James were ambushed by Covenant Sangheili; James was lost in space, and Linda was critically wounded. John saved four other Marines on the station, including Staff Sergeant Avery Johnson. The team returned to the UNSC Pillar of Autumn and was placed into cryo-sleep as the ship landed on, then fled Reach and, following the Cole Protocol, jumped into Slipspace with coordinates deduced by Cortana from constellation data retrieved earlier, in hopes of leading the Covenant away from Earth.
That is what he was doing according to the books. In the game, he is in cryo-sleep.