Tile Water Damage in Bathroom - Toilet?

I noticed today a significant area of slate tile around the toilet (about a 2' x 4' area) was discolored, and had perhaps lime deposits where water had dried...as well as flaking of the tile, and some rust and darkening. Clearly some sort of water damage. We pulled off the toilet and was surprised the under the tank itself, it seemed fairly dry. Wax seal looks a mess - not sure what the rubber flange should look like to know if it was in tact or not. Toilet was caulked.

What do I do now? This is a three story unit, so I can not see the floor under the toilet.

Do I replace the wax ring and toilet and wait and see? Or, do I remove some tiles and look deeper?

The flange is rubber??? check and see if it is a broken plastic flange that is moving on you.