Well, perhaps in the moment of Harry's death, a powerful dark magic from the Harry Potter world collided with a strange space - time anomaly in the Naruto universe. This catapulted his essence into Naruto's seal. Inside the seal, Harry could be a source of new wisdom for Naruto. He could teach Naruto about things like loyalty and sacrifice from his own experiences. And he might also gain some of Naruto's positive traits, like his unwavering determination, which could help him in his new 'afterlife' within the seal.
He could develop the ability to use chakra. Since he's in the Naruto universe now, he might figure out how to manipulate chakra using his magical intuition. Maybe he could combine his Patronus charm with chakra to create a new kind of protective shield. Also, he could learn to move at high speeds like Naruto characters do, which would be a new ability for him considering he was mainly using apparition in his own world.
The interaction between Harry's ghost and Naruto's seal in this fanfiction could be really complex. Harry's ghost might initially be confused when it ends up near Naruto's seal. It may not understand the nature of the seal at first. However, as it observes, it might notice the flow of chakra within the seal. If Harry had some knowledge of sealing magic in his own world, he might try to compare it to what he sees in Naruto's seal. His ghost could also potentially be a catalyst for some change in the seal. Maybe it causes the seal to react in a way that it has never reacted before, which could either be a good or a bad thing depending on the context of the fanfiction.
One consequence could be that it disrupts the balance of chakra within the seal. This might lead to Naruto having some issues with his power control or even cause the seal to weaken or malfunction.
One possible storyline could be that Naruto is faced with an overwhelmingly powerful enemy that he realizes can't be defeated any other way. So, in a selfless act, he decides to use the Reaper Death Seal. This would be a very tragic end for Naruto as he has so many friends and a family to live for. His death would likely send shockwaves through the Hidden Leaf Village and among his friends like Sasuke, Sakura, and Kakashi. They would be devastated, and it might also lead to a power vacuum in the village, causing all sorts of political and social unrest.
If Harry is stuck in Naruto's seal in fanfiction, he could potentially discover new forms of energy or power. Since he's used to magic, being in the seal might expose him to different types of energy like chakra in a very direct way. He could also make friends with the entities inside the seal, who could teach him things about Naruto's world that he would never have known otherwise. This could give him an edge when he finally gets out of the seal and has to interact with Naruto and the others.
Harry could try to communicate with the entities in the seal. By making allies, they might help him survive. For example, if he befriends a chakra - based spirit, it could guide him on how to get the resources he needs, like food (in a spiritual sense perhaps) or a safe place to stay within the seal.
Naruto might become bitter. After being alone, he could start to question all the values he once held. He may think that his efforts to protect and connect with others were in vain, which could lead to a cynical view of the world.
Another aspect in such fanfictions could be the origin of the Kyuubi seal. Some writers might delve into ancient ninja secrets and forgotten jutsu that were used to create the seal in the first place. They might also explore if there were other possible ways to seal the Kyuubi that were considered but not used. This can add a whole new layer of mystery and intrigue to the Naruto universe.
For Hinata, it would be a devastating blow. She loved Naruto deeply. She might become withdrawn and lose her usual gentle strength. Shikamaru, being Naruto's friend, would be angry at first, feeling that Naruto's sacrifice was unnecessary. But then he would realize the gravity of the situation Naruto faced. His death would also impact the younger generation. Boruto, in this fanfiction's context, would grow up without his father, and this would shape his character in a different way, perhaps making him more determined to carry on Naruto's legacy.