Perhaps in the fanfiction, Naruto loses his memories and thinks he's an ordinary villager. But then strange things start to happen around him that draw him back into the ninja world. He has to figure out his connection to it without his memories, which could lead to some really cool mystery and adventure elements.
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.
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.
The plot could also involve Naruto's memory loss being a result of some sort of dark magic or curse. And the male character in the Yaoi relationship has to go on a journey to find a way to restore Naruto's memories. During this journey, they grow closer and their relationship deepens in ways it wouldn't have if Naruto hadn't lost his memories. Their shared experiences during this time create a stronger emotional bond between them.
Obviously Naruto himself is the central character since the story is about him losing his memories. Sakura would likely be involved too. She's one of Naruto's closest friends and a medic - ninja, so she might try to find a way to restore his memories.
In some fanfictions, Naruto's lost memories and the fox are related to an ancient prophecy. The story could be that Naruto was meant to forget his past life as part of a grand plan to defeat a great evil. The fox, being a powerful and mysterious entity, has its own motives in all this. It might be trying to guide Naruto in a certain direction while he's clueless about his identity. His friends notice his strange behavior and start to investigate. Along the way, they uncover secrets about Naruto's past that even he didn't know, and the fox is at the center of it all, holding the key to his true self and the future of the ninja world.
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.
The village elders might see Naruto's memory loss as a threat to the village if they think it affects his ability to protect it. They could try to keep an eye on Naruto and the male character he is involved with in the Yaoi relationship. This could create tension as the two just want to figure out Naruto's situation and develop their relationship, but now they have to deal with the watchful eyes of the elders.
Perhaps in the fanfiction, Poison Ivy has developed a new type of plant toxin that can neutralize Batman's gadgets and physical abilities. For example, it could corrode his Bat - suit and make his grappling hook malfunction. Without his usual tools and skills, Batman would struggle and ultimately lose to her devious plans.
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.
One interesting plot could be Naruto finding out about his mother's clan and their unique abilities. Maybe he discovers a hidden jutsu passed down in her family that he can then learn and use to his advantage in battles.
In some fanfictions, Naruto's sister could be in a coma due to a curse. Naruto discovers a rare herb or a special chakra technique that has the potential to wake her up. He has to overcome many challenges, including political opposition within the Hidden Leaf Village who think he's wasting resources on his sister.