The story could also focus on the efforts to unseal Naruto. His friends and the characters from the crossover world could embark on a dangerous journey to find the key or the magic to break the seal. In a Naruto - Harry Potter crossover, Hermione might use her vast knowledge of magic to research a way to free Naruto from the seal.
One interesting idea could be the combination of Naruto's world with another popular anime world. For example, if it's crossed with One Piece, Naruto might use his sealing jutsu on Devil Fruits to prevent their misuse. It could also involve Naruto being sealed in a different realm from another anime and having to find a way back while facing new challenges.
A corrupt leader from a political - based crossover world might be the main antagonist. He views Naruto as a threat to his power, especially with the mystery of his seal. So, he tries to either keep Naruto sealed away permanently or use the situation to gain more control over his own people by creating fear around Naruto's presence in their world.
Another option is that a new character introduced in the crossover could be the main character. For instance, in a Naruto - Fullmetal Alchemist crossover, an alchemist from the FMA world could stumble upon Naruto's sealed state and make it their mission to free him, while also getting involved in the politics and power struggles of the Naruto world.
Obviously Naruto himself is a main character. Often, characters from the crossover universe are also main characters. For example, if it's a Naruto and Dragon Ball Z crossover, Goku might be a main character. He could interact with Naruto who has been sealed in a different way due to some strange event that connects the two universes.
One idea could be the exploration of how Naruto's sealing affects the crossovers. For example, if it's a crossover with the Bleach universe, the seal might disrupt the spiritual balance there. Another could be Naruto being sealed in a different dimension where the crossover characters reside, and he has to find a way to break the seal while interacting with these new characters.
In many such fanfictions, it could be a variety of deities. It might be an ancient and powerful god from Naruto's world's mythology that the story's author has chosen to insert. For example, it could be a god of elements like a super - powerful fire god, which could give Naruto even more control over his existing fire - based jutsu and new, more extreme abilities related to fire.
In some fanfictions, Kushina was sealed into Naruto through a complex jutsu. It might be a modified version of the sealing jutsu used to seal the Nine - Tails. The process could involve special incantations and chakra manipulations.
In some Naruto fanfictions, Madara might be sealed through a powerful jutsu created by the main character. For example, the protagonist could combine different elemental chakra natures to form a unique sealing technique specifically designed to counter Madara's power.
Well, in some Naruto fanfictions, Bardock might be sealed by powerful jutsu. Maybe a dark ninja uses a forbidden sealing technique to lock him away, preventing him from interfering with their evil plans.