I don’t think so. Cortana’s clearly changed since the last time we saw her, but I think it’s still technically Cortana. I have two theories as to why she’s a villain now.
1. She fragmented her rampant selves and scattered them all over the Didact’s ship in Halo 4, which tried an emergency slipspace jump after being blown up by the nuke. It’s very likely that the pieces that made it onto Genesis contained only the rampant fragments of Cortana, which were subsequently purified. There’s some evidence of this in Halo: Tales from Slipspace, Dominion Splinter. Almost immediately after encountering Warden and the Domain, she stalls the Warden and sneakily enters the Domain, which is something the old Cortana would do. However, after doing so, her other fragments enter as well and steal control of the Domain from Warden. This is NOT something the original Cortana would do, who was more curious than controlling. This tells me that even after being cured by the Domain, rampant AI retain parts of their rampant personality.
2. The Domain itself was what corrupted Cortana. The Forerunners were extremely arrogant. They saw themselves as the watchers of the galaxy, the holders of the Mantle of Responsibility. While technically a Precursor creation, by the time Cortana reached it, it was mostly full of Forerunner records. In the Halopedia article for the Domain is said to contain ancestral impressions and memories, and is regarded as almost living. It’s very plausible that such memories were accessed by Cortana and she in turn, inherited the Forerunners’ arrogance.
These are just my two cents. They may be wrong, maybe 343 just wanted Cortana to be the villain just for the shock value.
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