A really interesting plot could be a time - travel one. Rukia somehow travels back in time to Naruto's childhood. She sees the lonely Naruto and decides to help him. She secretly trains him in some of her shinigami techniques, which Naruto then incorporates into his ninja style. This changes the course of Naruto's life and how he approaches his ninja training, and they form a deep connection along the way.
One plot idea could be a crossover adventure where Naruto and Rukia team up to face a powerful new enemy. Maybe they meet in a strange in - between world and have to combine their unique skills to survive. Another idea is a story where they exchange their powers for a short time and have to learn to adapt to each other's abilities in a comical yet challenging way.
One idea could be that Ichigo and Rukia find themselves in an alternate universe where their roles are reversed. Rukia could be the one with the Shinigami powers from the start in Karakura Town, and Ichigo is a normal human who gradually discovers his own latent spiritual abilities to help her. Another could be that they are sent on a special mission together to a realm neither has been to before, like a dimension full of lost souls. There, they have to rely on each other more than ever to find their way back and complete their task.
Another plot could be that there's a powerful enemy who tries to use Rukia and Ichigo's feelings against them. They have to fight not only the external threat but also their own growing desires for each other, which leads to some tense and steamy moments in the fanfiction.
A plot could revolve around Sesshomaru being intrigued by Naruto's determination. Sesshomaru decides to train Naruto in some of his own combat techniques, which Naruto adapts to his own fighting style. In return, Naruto shows Sesshomaru the value of friendship and loyalty within a village. This could lead to Sesshomaru having a change of heart about his own solitary ways. Also, they could team up to face a common foe from Sesshomaru's world that has somehow entered the Naruto universe.
One idea could be that Naruto and Kashuina meet during a mission outside of Konoha. They start off as rivals, constantly trying to outdo each other in combat skills. But as they face various challenges together, they gradually develop a mutual respect and then deeper feelings. Another plot could be set in a post - war scenario where Naruto, now a hero, meets Kashuina who has a unique ability to heal the psychological scars of the war - torn ninjas. Their interaction then leads to a romantic relationship. And a third idea is that they are both students under a new sensei who pairs them up for special training. During this training, they discover things about each other that they never knew before and fall in love.
One idea could be Naruto being sent to the world of Death Note. He could use his ninja skills to try and outwit Light Yagami. Maybe he would initially be confused by the Death Note's power but then use his determination to stop Light from his killing spree. Another plot could involve Naruto meeting the Shinigami. He might learn about the balance between life and death in this new context and try to find a way to bring some of his ninja world's values to this strange new world.
Perhaps Naruto and Lala meet during a mission where Naruto is sent to a different dimension. Lala, being from an alien world, is intrigued by Naruto's determination and they form an alliance to face a common enemy in that dimension. Their different powers and abilities complement each other, and as they work together, they start to develop feelings for each other.
A more complex plot could be that there is a prophecy in both worlds about a union between someone from the Naruto universe and someone from Ruby's universe. Naruto and Ruby are the ones fated to fulfill this prophecy. They initially don't get along but as they face various challenges together, they start to understand each other and fall in love, while also saving both their worlds in the process.
In a naruto x avatar fanfiction, there could be a scenario where the Akatsuki from Naruto's world teams up with some of the villains from the Avatar world. This would force Naruto and the Avatar (whichever one it may be) to put aside their differences and form an alliance with other characters from both worlds to stop this powerful and evil coalition.
One idea could be that a zombie virus spreads in the Naruto world. Naruto and his friends have to not only fight the zombies but also figure out how the virus started. Maybe Orochimaru was experimenting with dark jutsu and it went wrong.