A 99 coach would of had a rubber roof which over time can dry out and become porous allowing water to penetrate the rubber.
If you had a few coats added over the old rubber it may have help seal the roof.
The roof has a metal strip around it screwed into the rubber roof and the metal wrap down to the side walls.
The area at the top of ladder may be attached to the rear fiberglass cap and the seam is dried out allowing water into the under roof decking and its decomposition and rotting.
Here are some links for roof rebuild, maybe you only need to rebuild that area but I would check other area's for soft spots and see if a new roof job maybe necessary.
RV ROOF SULUTIONS
Click on the pictures to enlarge and you will see what might be going on with your roof.
MORE ON ROOFS
The ladder is supported by blocks of wood imbedded in the fiberglass cap on the back wall of cap and the top of ladder on roof part of cap.