Well, one possible plot could be that Harry's love is taken away due to some dark magic. Maybe an enemy casts a spell that makes his love forget about him. Another could be that Harry has to sacrifice his love for the greater good, like to save the wizarding world. And also, it might be that there's a misunderstanding between them that causes the loss of love.
It could be Voldemort. Voldemort might use Harry's love as a weapon against him. He could either kill her or turn her against Harry. Another possibility is Draco Malfoy. Maybe Draco tricks Harry's love into thinking he's a better choice. Or it could be a new, unknown dark wizard who targets Harry through his love.
Perhaps he is betrayed by those he trusts. In the original series, there were instances of betrayal, and if in the fanfiction this is amplified, for example, if the whole wizarding community turns against him unjustly. He might feel so alone and hopeless that he loses his will to live. Also, if he discovers some dark secrets about his past that make him question his own identity and worth, it could lead to this state.
Well, in this kind of fanfiction, it might be that Sakura loses Naruto because of a misunderstanding. Maybe some false rumors spread about her, and Naruto distances himself from her. Then Sakura has to find a way to clear her name and win back Naruto's trust. Or perhaps Naruto is influenced by some dark force that makes him turn away from Sakura, and she has to fight against this force to get him back.
Often in such fanfictions, the plot may involve a betrayal that pushes Harry over the edge. It could be a friend or a mentor who turns on him. This sudden shift in loyalty would shatter his world view. He has always relied on the support of those around him, and when that is taken away, it becomes difficult for him to stay sane. His actions would then become erratic as he struggles to come to terms with this new and cruel reality.
A possible plot is that Draco loses his memory and finds himself in an entirely different environment. Maybe he's found by a group of outcasts or muggles who have no idea about the wizarding world. As he tries to piece together his past, he discovers new things about himself and the world around him that he had never considered before. He could also develop new relationships outside of the pure - blood wizarding society he was used to, which would change his perspective once his memory returns.
One interesting plot could be Naruto forgetting all his ninja skills. So he has to start from scratch, relearning basic jutsus. This would make for a great character development arc as he discovers his old abilities in new ways.
His friends, Hermione and Ron, would surely help. Hermione with her intelligence and Ron with his loyalty.
Perhaps in the fanfiction, Harry loses hope when he is betrayed by someone close to him. It could be a friend from Hogwarts who turns on him for personal gain or out of fear. This betrayal makes him feel isolated and like his fight against evil has no meaning. He might then start to withdraw from the fight, stop using his magic, and become a shell of his former self.
If such a fanfiction exists, a possible plot could be a scenario where they both discover a deep, unexpected connection during a time of great turmoil in the wizarding world. Maybe they find solace in each other's company and gradually develop romantic feelings that lead to a more intimate relationship. However, this would be a very different take from the original story's focus on the battle against Voldemort and the growth of Harry as a wizard.
One possible plot could be Naruto losing his arm during a battle with a powerful new enemy. He then has to struggle with not only the physical loss but also the emotional and mental toll it takes on him as a ninja. He might have to learn new fighting techniques that don't rely on two arms.