Chances are its going to be very rusty under the plastic sills, will be worth taking them off completely to assess the damage. Also the factory sealent tends to hide a lot of rust too. Probably find under the arch trims it's going rusty too, very common problem.
As sills are structural you must get new panels welded in properly if you are going to address the problem. You can buy replacement sills to weld in yourself, or take it to a good garage if you're not too competent with a welder.
Ring around garages to get some ideas on price, unfortuneately it varies a lot area to area