This article contains spoilers for Halo episode 9.
One scene from Halo Infinite shows how the Halo TV series failed in its handling of the relationship between the Master Chief and Cortana. Many viewers were surprised by Cortana's origin in the Halo TV series, which revealed the smart AI was created from a flash-clone of Dr. Catherine Halsey herself. This is, however, actually canon to the game timeline — although one major element of Cortana's story was rewritten substantially.
Halo introduced a degree of conflict between Cortana and the Master Chief. In the games, Cortana was installed in the Master Chief's armor; in the Halo Paramount+ TV series, her chip was implanted in John-117's brain. Dr. Halsey planned for Cortana to expand and take over the Master Chief's mind, believing that by doing so she would create the ultimate super-soldier — a man with all the enhanced skills of a Spartan and the intelligence of Cortana. Halo episode 9 saw Cortana forced to fulfil her programming to ensure Silver Team survived a confrontation with the Covenant on Aspero. The Halo season 1 ending appeared to suggest Dr. Halsey was right; the combined power of the Master Chief and Cortana truly made them a force to be reckoned with.
Related: Halo Reveals The Real Reason Dr. Halsey Created Spartans
Unfortunately, this very idea works against everything the relationship between the Master Chief and Cortana is supposed to stand for. That's perfectly symbolized by a crucial cut-scene in Halo: Infinite, in which the Master Chief remembered his introduction to the smart AI in the main timeline. Dr. Halsey explained that Cortana would reside "between" the Master Chief's mind and his Mjolnir armor, directly communicating with his neural
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