One possible plot could be that Flitwick focuses on teaching Harry advanced charm spells. He might see Harry's potential and take it upon himself to train Harry privately, away from the prying eyes of Snape or other potentially hostile teachers. This could lead to Harry having a new set of skills that come in handy during battles.
In the fanfiction, Flitwick could train Harry to control his magic better. Harry often had issues with his magic flaring out of control. Flitwick, with his knowledge of magical theory, could guide Harry through exercises that help him master his magic. This would not only make Harry more powerful but also more confident in his abilities. As a result, Harry could face the challenges in the wizarding world more effectively.
Perhaps Flitwick trains Harry in the art of dueling specifically. He could introduce Harry to ancient dueling techniques that have been long forgotten. Harry would then be able to surprise his opponents, like Voldemort's followers, with these new moves. Flitwick, being an expert in charms, might use charms in unique ways during the training sessions to make Harry a more formidable dueler.
Maybe it's about Harry learning some advanced magic spells from Flitwick. Flitwick could be teaching Harry unique charms or how to use his wand more effectively.
It could strengthen Harry's relationship with the Hogwarts faculty. Since Flitwick is taking the time to train him, Harry might feel more connected to the school and its teachers. This could lead to him having more support from the faculty as a whole.
One possible plot could be that Bellatrix, in a strange turn of events, decides to train Harry in the Dark Arts not to turn him evil but to make him a more formidable opponent against Voldemort. She might see his potential and think that by teaching him some of the Dark Arts, he can better understand Voldemort's tactics.
It could be about Harry finding a secret training ground in the Chamber of Secrets. Maybe he discovers ancient spells or magical creatures there that help him train for upcoming battles against Voldemort.
Well, in fanfiction, Flitwick could be portrayed as having a deep understanding of ancient protective magic. He might use this knowledge to create a sort of magical perimeter around Harry. He could also enlist the help of other magical creatures or objects within Hogwarts that are known for their protective qualities. For instance, he could get the help of the house - elves, who have their own brand of magic that could be used to keep Harry out of harm's way. And he may constantly be on the lookout for any signs of danger directed at Harry, using his magical senses to detect any malicious intents.
Perhaps Flitwick discovers Harry has a natural aptitude for a particular type of magic that is not commonly taught. So he takes it upon himself to train Harry privately. This could lead to Harry having a special role in a future conflict, like being able to counter a dark magic spell that no one else can because of this special training.
In this fanfiction, Harry could learn a great deal of advanced magic from Flitwick. Maybe he would master some complex spells that are not taught in regular classes. For example, he could be taught the secrets of charm magic at a much deeper level, which would help him in his battles against the Dark Arts.
One possible plot could be that Sasori, with his unique skills in puppetry, decides to train Sakura in combat techniques that involve precise movements and control, much like how he controls his puppets. He might see potential in her that others overlook, perhaps her determination and ability to learn quickly.
Perhaps the fanfiction could be about Naruto training Percy in stealth. Percy, being a demigod, often charges into battle head - on. Naruto, on the other hand, is a master of stealth. He could teach Percy how to move quietly and undetected. This would be a great advantage for Percy when he has to infiltrate a monster's lair or spy on the enemy. The story could show Percy struggling at first but gradually getting better with Naruto's guidance.
Well, perhaps Percy could be learning some new and powerful combat skills from Chaos. Maybe Chaos teaches him to manipulate chaos energy in unique ways for battle.