It was clear in season 1 that Miss Minutes was loyal to the Time Variance Authority (TVA) and therefore to whoever was running it. We now know that it was the One Who Remained, a version of Kang, who designed it all. But we didn’t know the extent of his loyalty until he plotted the rise of another Kang variant, Victor Timely. (The cyclical reality created by the Left Behind he with his scientific knowledge and he Bringing this information to Victor Timely makes my brain itch.) Although Miss Minutes appears to be helping Ravonna Renslayer (Gugu Mbatha-Raw), we later learn that Ravonna may have been romantically involved with He Who Remains, but her His perceived love may not be so. It was mutual. This is what drives Miss Minutes on her quest to convince Victor to give her a physical body so they can spend quality, sexy time together.
Miss Minutes is all over this episode, giving herself a throwback makeover with her greyed-out look and parading around in public like a ghost. She even turns red in one scene. She clearly imagines herself as a human, although she reminds Victor that He Who Remains made her an AI friend with whom he can play chess. I think she really fell in love with He Who Remains when she let him write his own show.
The thing is, you can’t really blame him for thinking there’s something going on between them. I mean, the Remnant created him, gave him the autonomy to become the best version of himself, allowed him to gain sentience, and then trusted him to help him carry out his plans. As he said, they spent nights together talking and playing chess.