A great plot could be centered around a common enemy. There could be a new, powerful force that is a threat to both worlds. So, Naruto and the leaders from the different Clans in K Project have to work together. This would lead to interesting interactions, like Yata from K trying to learn ninja techniques from Sasuke. And also, the political systems of both worlds would clash, making for a complex and engaging story.
One idea could be that K has some unique jutsu that Naruto wants to learn. So he teams up with K to go on a journey to master this new type of jutsu. This could lead to a lot of fun interactions as Naruto's energetic and determined personality clashes and also meshes with K's own characteristics.
One possible plot could be that Naruto somehow gets transported to the world of the K Project. There, he meets the different clans and characters. Maybe he teams up with some of the Kings to fight a common enemy that threatens both his world and the K Project world.
Perhaps a Dark Eldar wych could form an unlikely alliance with a Space Marine. Maybe the wych has a personal vendetta against a chaos warband that is also targeting the Space Marine's chapter, and they decide to work together to take down the common enemy. This would involve a lot of tense moments as they try to trust each other despite their very different cultures and motives.
Perhaps an Imperial Inquisitor ends up in the Star Wars galaxy and tries to manipulate the Sith and Jedi for his own ends. He could see the Sith as a useful tool, not realizing how dangerous they truly are until it's almost too late. This could lead to a three - way battle between the Inquisitor, the Sith, and the Jedi.
I think Naruto and Yata would be an interesting pairing. Naruto's energetic and positive personality could contrast with Yata's somewhat hot - headed nature. They could learn a lot from each other. Naruto could teach Yata about perseverance, and Yata could show Naruto some of his skateboarding tricks.
One interesting plot could be Naruto's ninja skills being used in the grimdark universe of Warhammer 40k. For example, his shadow clone jutsu could be a great asset in battles against the various alien threats in 40k. He could create hordes of clones to overwhelm the enemy forces like the Tyranids or Orks. Also, his ability to sense chakra might be similar to the psykers' ability to sense the warp, which could lead to some unique interactions with the Imperium's psykers or the Chaos sorcerers.
One interesting plot idea could be a crossover where Naruto's senjutsu abilities are combined with another universe's magic system. For example, if he were to cross over into the Harry Potter universe, he could use senjutsu to enhance his magic or even teach the wizards about chakra. Another idea is a crossover with the Dragon Ball universe, where Naruto's senjutsu clashes with the ki energy of the Saiyans. Maybe he has to use senjutsu to face off against a powerful Saiyan who has come to the Naruto world. Or a crossover with the Bleach universe, and Naruto uses senjutsu to interact with the spiritual energy there, perhaps even helping Ichigo in a battle against a powerful Hollow by using his unique senjutsu skills.
One plot idea could be that Naruto characters end up in Ikebukuro. For example, Naruto himself could be searching for a new type of ninja tool that he heard can only be found in Ikebukuro. Meanwhile, the gangs in Durarara start to notice this strange, orange - clad boy with strange powers. Another idea is a character swap where some of the Durarara characters gain ninja abilities and get involved in Naruto - style battles in their own world. Maybe Celty could use her shadow powers in a more ninja - like way, like stealth and quick attacks.
One idea could be that Naruto characters are transported into the Splatoon world. They might initially be confused by the ink-based battles and the unique species. For example, Naruto could mistake an Inkling for a strange ninja from another land and challenge them to a friendly spar, only to find out about the ink shooting mechanism. Another plot could involve the Akatsuki from Naruto trying to steal the valuable ink resources in the Splatoon world for their own purposes. They would face off against the Splatoon heroes who are determined to protect their world's resources.
A cool plot could be that there's a tournament across different anime worlds, and Inuyasha and Naruto are chosen to represent their respective worlds. Along the way, they discover similarities in their pasts, like both having some form of demon - related heritage (Naruto with the Nine - Tails and Inuyasha being a half - demon). They also exchange combat techniques. Naruto teaches Inuyasha how to better use chakra control in his attacks, and Inuyasha shows Naruto some unique sword - fighting skills.