In the final of Halo Season 1, the Master Chief leaves control of his consciousness to Cortana to defeat The Covenent, but it is not clear whether he is finally gone or not.
After a fight between the Master Chief and his Spartans, Makee takes the opportunity to establish a base and escape back to the Covenant.
There, Makee will use Forerunner technology within the bases to create a star map that shows the way to Halo.
However, the Master Chief and his Silver Team of Spartans tracked them down and attacked the site to initiate activation.
In the final of Halo Season 1, the Master Chief is drawn into a different vision with Make when he touches the base, causing Kaie to kill him so he can get out and back into battle.
After his release, the Master Chief discovers that he is no longer able to face only the forces of The Convenant and needs further assistance.
However, Cortana is an artificial intelligence programmed for learning and growth that is reluctant to take control and says it cannot bring back the Master Chief.
Before he dies, he says, "I believe you," and lets Cortana use his body to help defeat the Covenant units so they can escape (with the cornerstones).