Jack wants to know just how a door frame is made, so that he can take his apart. The sill is rotten.
Usually, but not always, the sill goes right under the vertical framing. Sometimes the vertical piece is notched into the sill. In either case, you have to either cut out all the rotten wood, or treat any part that has active fungus. The good news is that it is actually possible now, with special epoxies, to rebuild the whole rotten area without removing much of anything.
Minwax makes a Wood Hardener and BCS a liquid wood epoxy that you use to solidify the rotten wood and kill off the fungus. 
Then the BCS system goes futurer with an epoxy putty that fills in any missing wood. these are often used for door and window sills, as well as for rebuilding the bottom of wooden columns and porch rails.
A unique use for these is to repair rotten joists under toilets. The Minwax hardener will kill all the fungus and stop all changes in the wood allowing for sistering other joists to the side of the rotten ones. The BCS product properly applied can even restore the origional joist to its previsous strength.
Follow this link for details and working techniques when working with these penetrating epoxies.