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.
Perhaps Naruto arrives in the Warhammer 40k universe during a time of great crisis, like a major Chaos incursion. His strong willpower, which is similar to the determination of the Space Marines in a way, could inspire the Imperium's forces. He could also teach some of his ninja techniques to the Imperial Guard, like stealth and evasion tactics. In return, he could learn about the advanced weaponry and strategic warfare of the 40k universe, and together they could fight against the Chaos forces that are threatening to destroy everything.
A possible plot is that Naruto is transported to the Warhammer 40k universe and is mistaken for a powerful psyker. The Imperium might try to either recruit him or eliminate him depending on how they perceive his powers. Naruto, not understanding the complex politics and religious dogma of the 40k universe, would have to navigate through different factions while trying to find a way back home. Along the way, he could learn about the different technologies and cultures in the 40k universe and use his ninja knowledge to his advantage.
One interesting concept is the crossover with other popular sci - fi universes. For example, a crossover with Star Wars could have the Imperium of Man facing off against the Galactic Empire. Another concept could be the combination of different Warhammer 40k factions in unexpected ways within the fanfiction. Maybe the Space Marines teaming up with the Orks against a greater threat.
One interesting plot twist could be the combination of the Force from Star Wars with the psychic powers in Warhammer 40k. Imagine a Jedi using his Force powers in the grim and dark universe of 40k, facing off against Chaos psykers. Another could be the appearance of Imperial Stormtroopers in a Warhammer 40k battle, their white armor standing out among the chaos. Maybe they could be mistaken for some sort of new xenos threat at first. And a third plot twist might be the discovery of a lost Star Wars planet in the Warhammer 40k galaxy, full of unique technology and species that both sides would be eager to control or destroy.
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.
One idea could be that Naruto characters are transported to the Warhammer universe. For example, Naruto himself could be mistaken for a powerful chaos warrior due to his chakra. He might then have to prove that he's not a threat while also trying to find a way back home. Another plot could involve the shinobi clans of Naruto being compared to the different factions in Warhammer. The Uchiha with their Sharingan could be seen as having a similar level of mystery and power as some of the Warhammer sorcerers.
One idea could be a crossover with the Star Trek universe. The Tyranids could be seen as an extremely hostile alien force that the Federation has to deal with. Their bio - ships and swarming tactics would be a huge contrast to the more technological - based Starfleet.
Some interesting concepts are the different power sources. In Halo, we have things like plasma and fusion power, while Warhammer 40k has the Warp and its associated powers. How would these interact? Maybe a UNSC ship powered by a fusion reactor has to deal with the unpredictable effects of the Warp when it enters a region influenced by it. And then there's the concept of heroism. Spartans are known for their individual heroics, while in Warhammer 40k, heroism often comes with a heavy price and a lot of religious and ideological baggage. Combining these two views of heroism can make for some thought - provoking stories.
Some interesting concepts include the combination of the different power systems. In Halo, you have the MJOLNIR armor with its energy shields, and in Warhammer 40k, there are psykers with their psychic powers. Imagine a scenario where a Spartan with MJOLNIR armor has to face a Warhammer 40k psyker. How would their powers interact? Another concept is the cultural exchange between the two universes. The military hierarchies and honor codes in both settings could lead to some really complex and engaging storylines when combined.
One interesting idea could be the combination of Naruto's ninja abilities with the high - tech and grimdark elements of Warhammer 40k. For example, Naruto's shadow clone jutsu might be used in a unique way on the battlefields of the 41st millennium. Maybe the clones could be used to infiltrate enemy lines or to overwhelm ork mobs.
Well, it could be about a character who was once an ordinary person on a peaceful planet. But then, after being reborn in the Warhammer 40k universe, they find themselves in the middle of a battle against the xenos. They might have to quickly learn to use the advanced weaponry of the Imperium and fight alongside the Space Marines to survive. Their main plot could be centered around their journey to become a respected figure in the Imperium while constantly facing threats from all sides.