Hello! "With" is a preposition. In proper English, you are technically not supposed to end a sentence with a preposition. However, it is now more widely accepted to do so. "With" is actually unnecessary to use here. "A couple of hours later it is all over." would be the same as saying "A couple of hours later it is all done/completed/finished."

It means that whatever you are talking about is finished in 2 hours, eg a film, festival, market etc.