It's not clear from your post...is YOUR cat unneutered? If so, it's almost certainly contributing to his fighting and putting him at high risk of contracting FIV and/or FeLV, both fatal diseases, and of getting infected and abcesssed bite wounds (that's the same thing I'd say to anyone with an intact male cat who goes outdoors, so I'm not jumping on you, it's a stock answer...if I read wrong and your cat isn't an intact male, just disregard that last bit
If he's not neutered, he's in danger, and quite possibly in danger of inadvertantly hurting other cats)
As for the interloper...is there a way you can lock or block the catflap at night after your cat's come inside? Short of that, I can't see any way of stopping a cat from going where it pleases (they don't have much regard for human boundaries). They make cat-deterrent chemicals, but they don't work in all cases, and you may just end up offending your own cat with the smell. They also make catflaps that are locked and are only opened by an infrared tag worn on the cat's collar, but they are pricey.
You can call the local animal control agency, or trap the cat yourself and take it to a shelter or pound if you're sure it's a stray, though if it's truly vicious or tests positive for FIV/FeLV, it'll be euthanized (the same would happen to your cat if it was picked up and tested positive, BTW).
But locking or blocking the cat flap overnight is the best bet.