One plot twist could be that Snape's true motives for being at Hogwarts are revealed to be more about protecting Harry all along. Another could be that Harry discovers some long - lost family magic that he can only access with Snape's help. Maybe there's a secret prophecy that involves both of them as uncle and nephew, and it changes the course of the war against Voldemort.
Well, a major plot twist could be that Snape was actually the one who was supposed to take care of Harry after his parents' death, but due to some misinformation or dark magic interference, it didn't happen. Also, it could be that there are some dark family secrets that are tied to both of them. For instance, there could be a curse on their family line that only they can break together. And perhaps there's a hidden inheritance that Harry is supposed to get from Snape's side of the family, which Voldemort wants to steal, adding a new dimension to the fight against the Dark Lord.