Harry Potter himself could be the main character in a 'harry potter ninja assassin fanfiction'. Imagine if he discovered a hidden part of his heritage that involved ninja - like training. He could then use his new skills along with his magic to fight against Voldemort and his Death Eaters in a more stealthy and unexpected way.
It could be a new character, like an assassin from a far - off land who comes to Hogwarts under false pretenses. They have their own set of skills and motives that are different from the regular characters in the Harry Potter series.
The main antagonist could be an ancient evil spirit that has been awakened by the mixing of ninja and wizarding magic. This spirit is angry at the intrusion and starts to possess students and teachers at Hogwarts. The ninja and Harry Potter must figure out how to exorcise the spirit before it's too late and Hogwarts is completely taken over.
Perhaps an international wizard who has been trained in both magic and martial arts in some far - flung magical school. This wizard - assassin has his own code of ethics and when he meets Harry, he decides to take him under his wing, believing that Harry can be a force for good in a different way than the traditional Hogwarts - trained wizards.
It could be a rogue Death Eater who has mastered a new form of invisibility spell. This Death Eater might be seeking revenge on those who opposed Voldemort.
Hermione Granger could also be a main character. With her intelligence, she would be quick to learn ninja techniques and could even help improve them with her knowledge of magic. She might study the ancient ninja scrolls and find ways to combine the knowledge of both worlds for the greater good.
One interesting concept could be the combination of magic from the Harry Potter world and the stealth and combat skills of a ninja assassin. For example, a character might use a spell to enhance their ninja - like speed or invisibility while on a stealth mission. Another concept could be the clash of cultures, like how the Hogwarts houses' values might interact with the code of the ninja assassins.
It could be a former Auror who has turned to more shadowy ways of dealing with threats. After seeing the inefficiency of the Ministry's methods in some cases, they decide to take matters into their own hands and become a sort of assassin to target dark wizards.
How about Neville Longbottom? He could be the main character in a fanfiction set in the Chamber. Neville, who has always been underestimated, could show his true courage and strength. He might discover a hidden ability that helps him face the challenges in the Chamber, perhaps something related to his connection with plants, which could play a crucial role in defeating the Basilisk or whatever new threat is in the Chamber.
Hermione Granger would make a great main character in this crossover. Her intelligence would be useful in understanding the Assassin's Creed lore and how it relates to magic. Also, Altair Ibn - La'Ahad could be a main character. His wisdom as an Assassin could help the wizards in their fight against dark forces. And Ron Weasley could add some humor to the story while also being a valuable member of the team, using his wizarding skills along with the Assassin techniques.
One possibility could be a rogue Death Eater. They have the skills and the inclination towards dark magic. For example, Bellatrix Lestrange could have easily fit the role of a dark assassin. She was extremely powerful and had no qualms about using dark magic to achieve her ends.