The wax seal under the toilet had a leak, and the particle board got wet. This caused it to get soft and the toilet no longer had a solid floor to sit on. The toilet could move, and little bits of waste would seep through making the particle board even softer and weaker. This ended up rotting parts of the subfloor which I replaced with some...a ton of help. Thanks Robert!
While we were replacing the sub-floor it turns out the joists had been cut away back in the day to accommodate the new fangled plumbing. Here is what it looks like after we sistered a new 2x8 to the existing joist. You can see the end where it was cut for what looked like the waste water pipe from a sink. Above is the new subfloor of 3/4" 4ply plywood pounded in under the bottom plate.
This part of the room was not too bad, but if you are replacing the subfloor and you dont like the sink and counter......smash it out. This was the fun part, there was no toilet waste impregnated wood dust flying at me.