The rot could also be from the window sweating and condensation.
Depends on the material that the stool is made of. If it is wood, it could be cut out, patched, and re-painted. That is probably the easiest way if the moisture source was temporary.
If you have some carpentry skills and the stool is wood, you can get some stool board and re-cut and install a replacement.
If we are talking about a drywall return/sill, the advice would be similar to the first advice (dig out, clean up, patch, sand, prime, paint).
If you can post up a picture, you will get more directed feedback.