Halo season 2 will have to find a way to separate Cortana from Master Chief, but there are plenty of ways to make that happen. Based on the hugely popular video game series, Halo is the first live-action incarnation of the property featuring the game's main character, Master Chief, aka John-117 (Pablo Schreiber). Halo also features another fixture from the game, which is the AI known as Cortana. The CGI character in the show is voiced by Jen Taylor, who has provided the voice for Cortana throughout the game series.
In Halo season 1 it's revealed that Dr. Halsey (Natascha McElhone) has the intent of the Cortana AI being the next evolution of the Spartan program, which would have the enhanced humans fully controlled by AI. Dr. Halsey has Cortana installed into Master Chief's brain, where she begins her relationship with him in similar fashion to the games, but with far more growing pains than has ever been explored. Cortana is a learning AI, meaning that it evolves over time, gaining sentience along the way, which begins almost immediately in the show. Cortana comes to reject Dr. Halsey's plan to take over Master Chief, wanting only to help him, rather than control him.
In the Halo season 1 finale, as Master Chief is overwhelmed with soldiers from The Covenant and the rest of his team defeated, he turns to Cortana and asks her to take over, knowing it's the only way to defeat the enemy. Reluctantly, Cortana takes over Master Chief's consciousness and is able to take out the encroaching enemy, which seemingly erases John-117, leaving the AI in complete control—Dr. Halsey's plan all along. As the Spartans make their escape, Kai-125 addresses Master Chief, saying, "John, is that you?" to which Master Chief simply looks at her and then looks away, showing that Cortana is likely still in full control as the season ends. Halo season 2 has already been greenlit and Schreiber is expected to return, so the show will no doubt bring John-117 back, but the question will be how to do it.
How Halo Season 2 Can Resurrect John
In the Halo game series, Cortana actually picks John-117 to team up with, as the AI was allowed to do that. Cortana is installed in Master Chief's MJOLNIR Mark V armor (not his brain, as it is in the show). Since Cortana's installation is quite different in the show, the ways around resurrecting John-117's consciousness will be a little trickier. That said, since it's a new origin for their partnership altogether, the showrunners have every creative means at their disposal to bring John-117 back, which could be as simple as flipping a switch or as complex as a season-long journey to restore his consciousness. In the Halo game series, Cortana is frequently housed in a Data Crystal Chip, but also stores microscopic code within her holographic appearance. The data chip is installed in Master Chief's armor, which allows Cortana to assist in his missions, but she can also be taken out and plugged into other systems, allowing full control of everything from computer systems to weapons to ships and beyond.
Halo season 2 can separate Cortana in a number of ways, including the most obvious, which is to remove the chip that stores the AI from Master Chief's brain. This would likely restore John-117's consciousness and allow Cortana to be re-inserted in another way, perhaps traditionally, which is plugged into Master Chief's armor. However, the question would remain as to why the showrunners decided to install the AI in his brain to begin with if they were just going to take it out in the next season. Another route would be simply to have Cortana, a thinking, learning AI, find a way to separate from John-117 and exist without interrupting his mind (and body). A better possibility would be to somehow set Cortana free of being hardwired into anything in order to function, essentially making the AI "wireless". This would allow John-117 to remain in control of himself, but to have access to Cortana, which would be able to travel between systems in order to function at her absolute peak. One way or another, fans can rest assured that John-117 will be back in Halo season 2, but there are obviously many ways in which that can happen.