Thor and Loki eventually set out on a journey to go hunt the dragon together with Loki in Thor's body and Thor in Loki's. Because of the change in their bodies, Loki has to learn to use physical strength to his advantage and Thor reluctantly accepts that he has to use magic to aid Loki now that he's become the weaker of the two (by being in Loki's body). They learn to cooperate and manage to slay the dragon in the end, but one of them was seriously wounded in the process (I can't remember if it was the actual Loki or Thor in Loki's body). And as one of the brothers lay slowly dying, the magic that caused the body swap was suddenly lifted and they were changed back into their original bodies.
I think it had a happy ending with Thor and Loki learning to truly respect and appreciate each other. I can't really remember if they were in a relationship. Maybe it was focused more on brotherly love?
I've been trying to find this fic for a while now and any help would be greatly appreciated!