The Halo season 1 finale saw Master Chief relinquish control over his consciousness to Cortana in order to defeat The Covenent, but it's unclear if he's gone or not by the end.

After a battle between Master Chief and his fellow Spartans ensues, Makee takes the opportunity to steal the keystones and escapes back to The Covenant

There, Makee would use the Forerunner technology within the keystones to generate a star-map to show the way to the Halo.

However, Master Chief and his Silver Team of Spartans track them down, attacking the site just as the activation is started.

In the Halo season 1 finale, Master Chief is sucked into yet another vision with Makee when she touches the keystones, prompting Kai to kill her to set him free and get back in the fight.

Once freed, Master Chief finds that he's unable to take on The Covenant's forces alone, needing additional help.

Cortana, however, is an AI that's programmed to learn and grow is reluctant to take over, saying she may not be able to bring Master Chief back.

He says, "I trust you" before passing out, leaving Cortana to harness his body to help defeat The Covenant's troops and make their escape (with the keystones in tow).