There were a bunch of drones floating around, and decoys. Seemed to be pretty dense with soldiers too, so yeah, the poor aggressor might have been utterly outclassed. He barely even moved. It took me at least 10 seconds to get out of some equipment bay and somewhere with a view, after checking the map to see his general area (I read the hints!). I saw him dive for cover and waited for him to come out, another 15 seconds or so. I shifted position slightly, assuming he slipped past into the crates, but saw his head - he was lying on the ground, basically the same place I'd first seen him. pew
I don't even know what happens if you tranq someone in FOB. I just set all my guards to nonlethal on principle (~OCTOPUS ISLAND~) and did the same to this poor fellow. The base was alerted to his presence though, and I was advancing to a fresh position when he quit.
Maybe he would have had a chance against the highly-advanced defense force, if I hadn't been there to break his stealth.
Still wondering where the heck all this is in the menu, though. Is it supposed to be under Mother Base, or Missions? I get network issues pretty often so I kinda assume it just isn't showing up, but I did restart...