is most likely giving the stem cells the means to communicate with the ring builders
Oh snap, I didn't realize this. Yeah, I guess communicating with the local gatebuilder wifi would be standard design for all proto molecule alterations. I guess we see a little of this when he starts being able to read other people's minds.
Of course it’s always possible that the protomolecule was never removed from the stem cells
In this case he would have started puking and turning into a zombie. Followed by being tossed into a furnace with Cortazar.