We have just removed the laminate and subfloor in a bathroom. There was leakage from the toilet wax ring and the plywood is stained black. It is not soft at this time but I am concerned about mold. What do we do before we put down the underlayment?
Cut back and splice in new plywood any where you have any doubts about it. Shoot down a layer of 1/4" Hardie board in a layer of thinset over that, and tile to that. You will be happy. This is not rocket science, but tile won't stick as well to wood as you would like. The Hardie floor is both moisture barrier, and aid to leveling and fairing your floor for the tiles.