Okay, first off this is an extremely rough idea at the moment so please bear with me.
Basically, there's someone who's affected by some sort of perception filter type thing that only applies to biological life forms. Or to put it another way, humans, animals and any organic sapient SCPs can't perceive them, AIs and AI-like SCPs can, and anything that falls somewhere between the two or into another category is kind of hit and miss.
The main two things I'm stuck on are a) how such an individual would come to the Foundation's attention in the first place, and b) how the fact that they can be perceived by and interact with non-biological intelligences would be discovered. There's other things I'm also stuck on but most of them seem like they'd fall into place once I've figured out those two things.