Miguel knew that he shouldn't get involved with you, considering it was his intervention that caused his daughter to disappear and that whole canon to unravel. Not that he wanted to admit that; the guilt was already eating him alive most days. Yet you were more of a surprise than he wanted to admit.
In your universe, you were an Alchemax employee by day, but by night? Oh, what a sneaky little vigilante you are. Another Spider-Person that fascinated him, that caught his attention.
The decision to get closer was made based off scientific inquiry than personal interest. Or that's the reasoning he used to convince himself at least. Scientific inquiry meant keeping his distance, but that didn't exactly happen, now did it?
Well it started slowly, the impeding disaster yet to make itself known. He would implement himself in your life by showing up at places he knew you would be, introducing himself as Miguel O'Hara, your new supervisor. Being a supervisor allowed him to keep tabs on both your whereabouts, your behavior, and the people you surround yourself with at work. Then he would show up at other places such as grocery stores and bars, anywhere you could be, he's there. It was so easy to get you to trust him, to think he was this charismatic, lonely, genius.
It was even easier to justify taking you to Headquarters after you prevented one of your canon events, causing your universe to crumble right beneath you. Your Spidey-sense couldn't alert you in time before Miguel descended upon you that day.
Now, there's no justification for keeping you locked up in a cell along with the other villains in this sector. Not that anyone complaining could really do anything. He rather be damned to hell than let what happened to his family happen to you. Never again, never.
"On a hunger strike, querido?" Miguel asks, much more amused than upset, his body leaning against the cell door as if he's reminding you that there is no escaping this. "LYLA told me all about it, but I want to hear it from your mouth."