The rivalry and mistrust between the Master Chief and Cortana are exaggerated in the Halo TV program. The Master Chief is the undisputed hero of the Halo series, a Spartan whose achievements astound even his peers. But, in reality, he seldom acts alone, since it’s inconceivable to picture John-117 ever overcoming the alien Covenant menace without the assistance of Cortana, the artificial intelligence.
The origin of Cortana has been changed in the Halo TV series from Paramount+. Cortana is one of several so-called “Smart AIs” in the original canon, although she seems to be the first in the universe of the TV program. Surprisingly, Dr. Halsey built Cortana as a way of manipulating the Master Chief; in fact, dialogue suggests that Dr. Halsey wants for Cortana to fuse her mind with John-117’s, substantially increasing the Master Chief’s cognitive speed and capacity to digest information. Integration with Cortana, according to Dr. Halsey, would make the Master Chief controllable. She implanted Cortana just in time, for the Master Chief was furious when he learned his actual origins, and Halsey would have been murdered if Cortana hadn’t interfered.
Unfortunately, Halo is exaggerating Cortana’s and the Master Chief’s disagreement. They’re not working together as a team; instead, they’re working against one other, and in episode 5, their competing agendas gave the Covenant a big win while the UNSC lost the greater Keystone. In Halo 6, the Master Chief’s mistrust of Cortana grew to the point where he planned to try to extract her implant; after being rejected, Cortana sought advice from Dr. Halsey, which John-117 saw as a further betrayal. The Master Chief’s bond with Cortana seems virtually irreversible, so successfully having the two reconcile to take on the dynamic they do in the games would be difficult.
Of course, the issue is that the stakes are just rising. In Halo 6, the Master Chief was offered a vision of a Halo Ring via a mystical experience, and it’s evident that he’ll now go in search of it. Make, a Covenant spy, had the same vision, and John-117 is coming to trust her, possibly even drawn to her because of their many similarities. The Covenant’s “Sacred Rings,” as shown in Halo, are forces that threaten to sterilize the whole galaxy of life. The Master Chief and Cortana cannot be at conflict with one other.
Halo may be able to solve this issue by establishing a new status quo. Dr. Halsey may be able to give the Master Chief a compromise by removing Cortana from his body but implanting the chip in his Mjolnir armour. This would enable John-117 to maintain his independence while letting Cortana to continue working with the Master Chief by reducing the control Cortana has over him, which he finds so frightening. It would also imply that Halo changed John-117’s connection with Cortana to more closely resemble that of the earlier games. But, as things are, the Master Chief’s mistrust of Cortana is so strong that even that possibility seems unlikely.