Perhaps the assassin is a double agent, and Moody's betrayal is part of a much larger scheme. The assassin could be pretending to be betrayed to gain the trust of the real villains. So, the assassin then uses this new - found trust to gather information and save the day in the end. Another plot twist could be that Moody is not the real Moody, but an impostor who betrays the assassin for reasons related to the impostor's true identity and motives.
I'm not sure of a specific one off the top of my head. But you could try searching on fanfic websites like FanFiction.net or Archive of Our Own. Use the keywords 'Harry Potter', 'assassin', 'betrayed' and 'Moody' in the search bar to narrow down the results.
Well, one possible motive could be that the assassin is working for Voldemort. Moody was a powerful Auror and a threat to Voldemort's plans. By eliminating him, it would clear the way for the Dark Lord's operations. Another motive might be personal revenge. Maybe Moody had put someone close to the assassin in Azkaban in the past, and this was a way to get back at him.
Maybe it's a character who has a hidden identity. It could be someone who was thought to be dead but actually survived and is now seeking revenge. This person could have a grudge against Moody for something that happened in the past. Or it could be a new character created specifically for the fanfic, a dark wizard from a far - off land who has been hired to kill Moody.
In these fanfictions, a really cool plot twist could be that Moody, because of his experience with the dark arts, has knowledge of a secret power within Harry that even Voldemort doesn't know about. He nurtures this power in Harry, which makes Harry a completely different kind of threat to the dark forces. Maybe it's a power related to the ancient magic of the founders of Hogwarts that was passed down in a way no one expected.
In a 'Harry Potter betrayed fanfic', perhaps Hermione turns against Harry. It could be because she disagrees with Harry's more dangerous and reckless plans to fight Voldemort. She might think he's endangering too many lives without proper thought, and this leads to a rift and a sense of betrayal.
A possible plot twist could be that the grandmother is actually a Death Eater in disguise. Little Red Riding Hood thinks she's going to visit her sweet old grandma, but when she arrives, she discovers the dark truth. Another twist could be that the red hood she wears is a Horcrux. This would add a whole new level of danger and mystery to the story.
Perhaps Moody, being a very experienced Auror, trains Harry in some dark magic defense techniques that are not taught at Hogwarts. This gives Harry an edge in fighting the dark forces but also makes the Hogwarts faculty a bit wary of him. He could then be in a situation where he has to prove that his knowledge is for good and not for dark purposes.
In a 'Harry Potter is an assassin' fanfic, the plot could start with Harry being trained by an unknown and powerful wizard who has his own motives for creating an assassin out of Harry. This trainer could be someone from a far - off land or an ancient order. Harry then starts taking on targets within the wizarding world that are supposedly 'evil' but as he delves deeper, he realizes that things are not as black and white as he was told. His friends start to notice his strange behavior and he has to either come clean or keep lying to them. As the story progresses, Harry might have to make some tough choices between his loyalty to his friends and his new - found assassin duties, all while uncovering secrets about the wizarding world that were previously hidden.
One possible plot twist could be that the troll is actually under the control of a dark wizard. So when Harry saves Hermione, they realize that there is a much bigger threat at hand. Another twist could be that the troll turns out to be a transformed Hogwarts student, and they have to find a way to reverse the spell instead of just fighting it.
Maybe he would be trained to be a super - powerful dark wizard. However, his natural good - heartedness, which he got from his parents, starts to shine through. This could lead to a conflict within the Death Eater community. He might be seen as a threat to their ideology and have to fight for his life against those who raised him.