Over time, one of several things can happen to screw up this wonderful feat of engineering. Twigs, leaves and squirrel droppings can clog up the drains. The water has nowhere to go but into the headliner and then into the passenger compartment of the car.
The other thing we’ve seen is that the tube can become disconnected and actually separate from the drain. In that case, the water does the same thing and obeys gravity.
So, I’d ask your mechanic to check your moon roof drains. He’ll test them and see if water is draining properly. If not, he can try to gently blow them out with compressed air, which may fix the problem.
If your moon roof drains are all working perfectly (which they’re probably not), the next suspect would be the rubber seals around the rear passenger door. If part of the seal that’s designed to keep water, wind and noise out got torn or damaged, that could allow water to seep in around that door and get on the floor back there.
It’s going to be one of those two things, Margo, so get them checked out. Then you can write back to us and ask us how to get a horrific smell out of a 2009 Lincoln Town Car that had a long-term water leak.