It was clear in season 1 that Miss Minutes was loyal to the Time Variance Authority (TVA) and, by extension, whoever was running it. We know now that it was the Kang-variant He Who Remains who engineered the entire thing. However, we didn’t know the extent of her loyalty until she engineers the rise of another Kang variant, Victor Timely. (The circular fact that a He Who Remains created her with his scientific knowledge, and that she brought that knowledge to Victor Timely makes my brain itch.) Though Miss Minutes appears to be helping Ravonna Renslayer (Gugu Mbatha-Raw), we later find out Ravonna may have had a romantic relationship with He Who Remains, though her perceived love may not have been reciprocated. That’s what sets Miss Minutes off on her quest to convince Victor to give her a physical body so they can … um … spend some quality sexy time together.
Miss Minutes is all over this episode, giving herself an old-timey makeover with her grayed-out appearance and showing off as a ghost in public. She even blushes in one scene. She clearly imagines herself as a human, despite the fact that she reminds Victor that He Who Remains made her as an AI companion to play chess with. I think she actually fell in love with He Who Remains when he let her write her own program.
The thing is, you can’t really blame her for thinking there is something between them. I mean, He Who Remains created her, gave her autonomy to become the best version of herself, allowed her to gain sentience, and then trusted her with helping him carry out his plans. As she says, they spent night after night together, talking and playing chess for eons.