Well, it looks like you’ve got some great ideas so far, but if you want to make the animal sanctum play a key role in the story, what if you somehow tie in the endangered animal refuge with the memory experiments
Maybe Dr. Arrowood started on his quest to erase/replace memories because poachers keep on returning to the site and stealing the rare animals he’s worked for years to protect. Maybe stealing and selling the animals, or their parts, is a hugely profitable business, and now Dr Arrowood has got on the bad side of the boss of one of the smuggling outfits, or some such thing. He’s willing to trade memory-wiping secrets in exchange for keeping his animals and his sanctuary safe. (I can imagine a major crime boss would have plenty of ways to use drugs or technology that would erase people’s memories.) And then maybe he finds himself in over his head, and stuck fulfilling promises he never meant to keep…and he hates himself for doing what he’s doing to Rubi and others, but if he stops, then everything he’s worked for will be destroyed and everyone, maybe even Rubi and others, will be killed. He tells himself he’s hurting a little part of her (stealing the memories) in order to save her life.
Too much help isn’t always helpful, but I thought I’d throw my two cents into the mix, because it’s such a cool story idea!