I am...so torn. On the one hand, seeing our former villain's struggle with his inner monster, his caring for the h, which had been there before he ever started experimenting... And yet, previous books indicated a complete lack of concern about anything or anyone. That's problem A. That until the end of the previous book, there was no indication he really concerned himself about others.
And then you find he's kept the h's comatose body in a penthouse for...an undetermined amount of time, because he cared about her.
(scratches head)
Problem B would be the sudden delving into the supernatural. Up until now, the theme was they used some method to give animal DNA to damaged humans to help them heal. 1) we have a flipping phoenix, 2) the other Dr has apparently turned into a vampire or demon or..something.
So the H has kept the h hooked up to equipment in his penthouse for...years. She's been in a coma since ODing 20 years before. Her parents died, and he ah...absconded with her before she got unhooked. Sleeping beauty has undergone his special treatments, yet remains comatose...until he makes the decision that he's got to hide evidence he was here and blows the penthouse. Since the h has turned into a phoenix of sorts, she's finally warm enough to come out of hibernation. He finds out she's alive after she's seen walking into burning buildings, starkers. He manages to catch her attention, bad guys show up, failed experiments show up, a not-so-failed experiment and his wife show up... Eventually they are sort of all together but still being tracked.
Just guessing here but equipping a room to be a lab, complete with hospital bed, would likely get someone's attention. Just also guessing but if your former partner sold you out, you probably should have changed all the locks immediately, so to speak, as it's likely he knew all your bolt holes.