A plot twist might be that Snape is actually under a spell or some kind of mind control that affects how he treats Harry as his master. Or perhaps, Harry finds out that Snape is not who he seems, and there's a whole other side to his personality that was hidden. It could also be that Snape's teaching methods lead Harry down a path that is unexpected, like exploring a forgotten branch of magic that has unforeseen consequences.
One possible plot twist could be that Snape has a hidden agenda all along. Maybe he's been using Harry as a pawn in a bigger scheme related to the wizarding world's power struggle. Another could be that Harry discovers a long - lost family connection to Snape that changes their dynamic completely.
One possible plot twist could be that Snape discovers some hidden magic in Harry that he didn't expect. Maybe a power that's related to the Potters but also has a connection to Snape's own family. Another twist could be that the other Potter family members don't approve of Snape adopting Harry, leading to a family feud within the wizarding world. And perhaps, there could be a dark force that tries to use Snape's new relationship with Harry against them.
One interesting plot twist could be that Snape's 'mastery' over Harry is actually a ruse to protect him from a greater evil. Snape, in his complex way, is using this guise to keep Harry close and train him in secret arts that Dumbledore didn't have the time or the nerve to teach Harry. This would turn the whole master - slave dynamic on its head and show Snape's true loyalty to Harry and the cause against Voldemort.
One possible plot twist could be that Snape blackmails Harry into joining a secret magical society at Hogwarts that Snape is leading. This society could be dedicated to protecting a powerful but dangerous magical artifact. Harry initially resists but realizes the importance of the cause as the story progresses.
One common plot twist is that Snape was forced to hide his fatherhood due to some dark magic threat. Another could be that Harry's mother had some sort of pre - arranged deal with Snape that led to Harry's birth.
A possible plot twist could be that Snape is actually the one who arranged for Harry to be sent to Azkaban, but for a noble reason. Maybe he knew that Harry was in danger from a more powerful dark force and Azkaban was the only place that could keep him safe temporarily. Another twist could be that the real culprit behind the crime Harry is accused of is someone very close to Snape, and Snape has to choose between protecting that person and helping Harry. It could also be that Snape discovers that Harry has a hidden power while in Azkaban that could change the fate of the wizarding world, and he now has to keep Harry alive at all costs.
Often, there's a plot twist where some magical interference or prophecy was involved in hiding the truth. Maybe a powerful wizard or witch cast a spell to make everyone believe Harry was James' son when in fact he was Snape's. And then, as the fanfiction unfolds, there are signs and clues that start to surface. Like, Snape's strange behavior towards Harry throughout the years at Hogwarts might be because he was his father but couldn't show it. It creates a really interesting re - imagining of the relationships in the 'Harry Potter' world.
One plot twist could be that Snape discovers Harry is his son right before a major battle. This new knowledge gives him the extra motivation to fight even harder to protect Harry. Another could be that Voldemort finds out about this relationship and tries to use it against them both, perhaps by threatening to harm Harry if Snape doesn't turn on Dumbledore.
In this type of fanfiction, a plot twist could be that Snape saves them, but they end up having to go into hiding in a completely unexpected place. Maybe they have to live among muggles in a way they never thought possible. Another plot twist could be that Snape saves them, but then realizes that he has put himself in a very dangerous position with Voldemort's followers. So he has to find a way to protect himself while also protecting Lily and James. And there could also be a plot twist where Snape saves them, but they don't believe his motives are pure and they try to escape from him, leading to a whole new set of adventures and challenges.
One plot twist might be that Snape has a secret weapon or power that he reveals at the last moment. For example, he could have a powerful protective charm that not only saves his life but also turns the situation around, making the marauders the ones in danger. Or perhaps there is a prophecy involved that the marauders were unaware of, and by trying to kill Snape, they are actually setting in motion a chain of events that will lead to their own downfall.
A possible plot twist could be that Merlin is not actually dead but has been trapped in a different dimension. Harry, as his son, has to find a way to free him. This would completely change the dynamic as they could then fight side by side against the forces of evil.