Regardless, there was enough of what looked like mold to warrent more than just painting it or putting flooring over it.
The fix was fairly straightforward. We cut out the area out piece by piece with the circular saw and occilating tool.
As can be seen above, there wasn't insulation in the middle cavity when we took the floor off (??) so we filled that in with some.
Right in the center of hallway is the tongue and grove floorboard has to allow for both expansion and added strength. Thankfully we were cutting from a full sheet of plywood, so we were able to use that edge. Unfortunately though, because we were patching a hole, we had to cut off the to tongue off on the other side.
So I made some braces for all the edges of the board on that side, as well as the middle, so there wouldn't be any sagging. You can see one of the middle ones fairly clearly in this pictures.
Once all the insulation and bracing was all set, we cut a board to size, and screwed it down. Much better!