Re: Tony's peeps
Osborn junior ran off with Mary Jane. From what Robert said, Gwen and her friends were looking for her, but the littlest Osborn was erratic and dangerous, which explains your entire little CPS fiasco. As for the facilities? Osborn was testing people. Someone killed him, but there were suspected facilities still out there. They might be operational, but I don't have that confirmed.
If I'm missing anything, Jason can probably fill it in. Last I heard, Mary Jane was still missing with Harry, and they were checking locations.