Maybe in this fanfic, when they enter Slytherin, they find out that there is a dark secret in the house's past that is related to Voldemort but not in the way everyone thought. They have to solve this mystery while also dealing with the prejudice from the other houses. It could lead to a situation where they use their Gryffindor - like courage within the Slytherin environment to uncover the truth and in the process, they change the whole dynamic of the Slytherin house.
One possible plot twist could be that they go into Slytherin and are initially shunned by the other Slytherins. But then they discover a hidden group within Slytherin that has different values from the traditional Slytherin ones. This group is more inclusive and values knowledge and friendship over pure - blood supremacy. Harry and Hermione then work with this group to change the perception of Slytherin within Hogwarts.
In this fanfiction, a great plot twist could be that the Slytherin character has a hidden identity as a member of an ancient magic - protecting group. The betrothal to Harry is part of a bigger plan to unite the houses against a new, emerging dark force. As they come together, they face a lot of opposition from both sides, Gryffindor and Slytherin, but through their relationship, they start to bridge the gap between the two houses.
Perhaps a plot twist could be related to memory modification. One of them has their memory modified in the past which affects their relationship in the present. For instance, Tonks might have had her memory modified by some dark magic and she forgets her previous relationship with Harry and Hermione. As they try to restore her memory, they discover secrets about their past together and it changes the course of their marriage.
A great plot twist could be related to the time - travel itself. What if the way time - travel works in the WW2 era is different from how it is in Harry's time? This could lead to him getting stuck or being unable to use his magic properly. Or perhaps he discovers that a certain event in WW2 was actually caused by a wizard from the future (not just him) who was trying to correct something in the wizarding world's past. His attempts to fix things could then make the situation even more complicated as he unknowingly steps on the toes of a much larger time - traveling plan.
Well, a really interesting plot twist could be Hermione's role in the Slytherin house. She could become a leader, using her intelligence to reform the house's more negative aspects. Or, she might be caught in the middle of a power struggle between different Slytherin factions. Also, her interactions with the Slytherin pure - blood families could be full of drama. Maybe she discovers a family secret that could change the whole wizarding world.
Perhaps Snape and Hermione were secretly working on a time - traveling potion project. Due to some unforeseen consequences of time manipulation, Hermione ended up pregnant. It could also be that a powerful magical artifact they were studying had some sort of fertility - enhancing effect that they didn't anticipate at first.
One possible plot twist could be that their relationship is a cover for a secret mission. They pretend to be dating to get close to an enemy who is targeting couples. So while they seem to be having normal dates, they are actually gathering intel.
One interesting plot twist could be that Harry uses his Slytherin cunning to reform the house's negative image. He might convince his housemates to abandon pure - blood supremacist ideas and focus on academic and magical achievements instead.
Perhaps a major plot twist is that the 'Prince of Slytherin' has a secret connection to Harry Potter. For example, they could be long - lost relatives. This would completely change the dynamic between Harry and the Slytherin character and lead to unexpected alliances and conflicts in the fanfic.
One interesting plot twist could be that Hermione, as a Gryffindor in the original series, starts to question the values of her own house because of her newfound admiration for Slytherin. Maybe she discovers a long - lost family connection to a Slytherin family, which makes her more empathetic towards their ways. Another could be that she uses Slytherin - like cunning to solve a problem that Gryffindor bravado couldn't handle, causing a rift between her and some of her Gryffindor friends.
Well, it could be that Merlin, with his powerful magic from his own legend, sees Harry as a threat in Slytherin. Maybe he's been influenced by some dark force in the Slytherin common room. And so, he decides to fight Harry. Harry, of course, would use his Gryffindor - like courage and the spells he's learned at Hogwarts to defend himself.