Well, one possible plot could be that Naruto somehow stumbles upon a portal or a hidden area in the Naruto world where Xenomorphs exist. Maybe Orochimaru was doing some forbidden experiments and accidentally opened a gateway to their dimension. Naruto, being the curious and brave ninja he is, decides to explore. He then has to use his ninja skills like his shadow clones and rasengan to fend off the Xenomorphs. He might also try to find a way to close the gateway to prevent the Xenomorphs from spreading across the ninja world.
The plot could be that Naruto discovers Pikachu in the Hidden Leaf Village. Maybe it was lost from the Pokémon world. Naruto, being the kind-hearted ninja he is, decides to take care of Pikachu. They then go on adventures together in the Naruto universe, with Pikachu using its electric attacks to help Naruto in battles against the bad guys.
The fanfic could start with Naruto being exposed to a strange chakra during a battle with an unknown foe. This chakra mutates his own and results in him getting the Rinnegan. As a result, he gains the ability to understand and communicate with all forms of life, which is one of the Rinnegan's powers. Naruto decides to use this new power to broker peace between different ninja clans and villages. He uses the Animal Path to summon various powerful beasts to act as ambassadors of peace. However, there are still some rogue elements in the ninja world who see Naruto's new power as a threat and try to eliminate him, leading to an all - out battle where Naruto must use his combined powers, including his new Rinnegan abilities, to defend himself and his ideals.
Maybe the Ninken is a special one with some sort of prophecy attached to it. Naruto gets the Ninken and at first doesn't understand its true significance. But as time goes on, he realizes that the Ninken is key to unlocking a new power within himself. The Ninken also has its own backstory that is slowly revealed as the story progresses, like it was once part of a great ninja's team and has been waiting for the right person to come along, which is Naruto.
One possible plot could be that Naruto discovers a strange gun in a hidden dungeon during one of his missions. He initially has no idea how to use it but as he studies it, he realizes it has some unique powers. Maybe it can shoot chakra - based bullets that can immobilize enemies stronger than him, which changes the way he approaches battles.
One possible plot could be that the UNSC discovers a derelict Xenomorph-infested ship while on a routine exploration mission in Halo space. The Spartan soldiers have to fight off the Xenomorphs while also trying to figure out how they got there and if there's a connection to the Forerunners. Maybe the Xenomorphs are being used as some sort of biological weapon by an unknown faction.
One possible plot could be that Naruto has to learn to control the Yin Kurama's power. He might face challenges like internal struggles as the Yin Kurama's more negative and chaotic energy tries to influence him. He could also have to use this new power to fight a powerful enemy that only the combined strength of his normal chakra and the Yin Kurama's power can defeat.
Another plot twist could be that Naruto getting the Sharingan is part of a much larger conspiracy. The Akatsuki might be behind it, trying to create a super - powerful being that they can control. So Naruto has to figure out who's behind this while also dealing with the new power. He might find that there are some hidden motives among his own allies as well, which would really shake up the story.
One possible plot twist could be that Naruto's stand has a power that is completely opposite to his normal ninja abilities. For example, if Naruto is known for his brute strength and large - scale attacks, his stand could have the power of stealth and infiltration, forcing him to adapt to a different style of combat. Another twist could be that the stand is linked to an ancient evil, and Naruto has to struggle not to be consumed by its power while still using it to protect his village.
One possible plot twist could be that the kidnappers are actually being controlled by an old enemy of Naruto's village who wants to use him as a bargaining chip to get some ancient scrolls. Another could be that Naruto is kidnapped by someone who thinks he is the key to a powerful jutsu they want to unlock, but in reality, they have the wrong idea about Naruto's abilities. Maybe the kidnappers are from a hidden group within the ninja world that has a grudge against the Uzumaki clan and Naruto specifically.
The plot could involve some sort of time - travel or alternate dimension scenario. Naruto could be sent to a parallel world where the Uchiha clan was never massacred. There, he befriends the Uchiha and learns their ways. Eventually, he earns the right to receive the Eternal Mangekyou Sharingan through his deeds and his strong bond with the clan. With this new power, he has to find a way to return to his own world and use it to protect his friends and village from a new, greater threat.