In terms of the overall plot, it could lead to a race against time. The characters will need to find a way to exorcise Vecna from Will quickly. This might involve seeking out new knowledge, perhaps from an unexpected source. Maybe an old character from the past who has some knowledge about Vecna's possession returns to help. It also opens up the possibility for new alliances and betrayals within the group as they struggle with this new situation.
Well, one possibility is that Will starts to have visions that Vecna uses to manipulate the other characters. He might show them false images of their worst fears, leading to chaos within the group. For example, he could make Eleven see herself losing her powers and being unable to protect her friends.
Well, a frequent theme is the change in Dipper's personality. When possessed, he could become more aggressive or withdrawn, which creates a contrast to his usual curious and determined self. There may be a theme of redemption too. If Dipper does something bad while possessed, the story could be about him making amends once he's free. And sometimes, the fanfiction might use the possession as a way to introduce new powers or abilities that Dipper has to learn to control.
A common theme is the battle for control. Harry is constantly fighting against the possessing entity for control over his body and mind. For example, in many fanfictions, he tries to resist using dark magic that the entity might force him to do.
One of the most likely possessing entities could be Bill Cipher. He's a powerful and malevolent being in the Gravity Falls universe, and he has shown an interest in Dipper before. Another possibility is an ancient spirit or demon from the forest around Gravity Falls. The forest is full of mysteries, and it's not hard to imagine some dark entity lurking there that decides to possess Dipper.
One common plotline is the struggle for control. Naruto has to fight against the entity possessing him, like in many fanfictions where he battles his own body's takeover. Another is the reaction of his friends. They usually try to find a way to save Naruto, which often involves researching ancient texts or seeking out powerful ninja who might know a solution.
One popular 'Naruto gets possessed' fanfiction is 'Possessed Naruto: The Dark Path'. In this fic, Naruto is possessed by a powerful and ancient spirit, which leads to a whole new set of challenges for him and his friends. Another one could be 'Naruto's Possession: A New Power Unleashed', where the possession actually gives Naruto some unexpected abilities that he has to learn to control.