My alligator gare fish is struggling, it's upside down.?

Could be a cut, internal bleeding, or internal parasites. I suggest you check your water, see if the nitrites and ammonia are too high. If they are, do a 25-50% water change, and then wait. Only time will tell at this point, and make sure he's not in a tank with other fish that can nip at him while he's injured.