I have a 99 Trooper S w/Auto trans. The car has 78k miles and today i heard a clunking/banging noise from what i believe is coming from the engine. Does anyone know what it might be and how long does the warranty cover

Have you check the oil recently?

you only have a 5yr or 60k warranty so it is long gone.

If you have oil on your dip stick it could be the S-Belt tensor is knocking around or the Timeing belt tensor knocking around.

The finally thing it could be is rod knock which means it is time to rebuild the engine (hence the quesiton of checking the oil).