A cool plot could be a time - travel story. What if Jotaro Kujo somehow ended up in the Naruto universe? He could use his Star Platinum to take on some of the powerful ninja there. Or perhaps Naruto travels to the Jojo universe and has to learn how to use Stands. He might befriend some of the Jojo characters and together they face off against the enemies in that world. Maybe Dio Brando discovers the power of chakra and tries to use it to enhance his vampire abilities, which would draw the attention of the Naruto characters who would then try to stop him.
One idea could be to have the Jojo characters enter a popular video game world like Minecraft. They could use their stands to build amazing structures or fight off mobs in unique ways. For example, Star Platinum could be used to mine blocks at super - fast speed.
One idea could be a crossover between 'Jojo' and 'Harry Potter'. Imagine Jotaro in Hogwarts, using Star Platinum to perform magic in a unique way. Another could be a 'Jojo' and 'My Hero Academia' crossover, where the stands of 'Jojo' characters interact with the quirks of 'My Hero Academia' characters. Or perhaps a 'Jojo' and 'Lord of the Rings' crossover, with Jojo characters on a quest in Middle - earth.
How about a story where the Avengers are pitted against Dio? The Avengers would have to deal with Dio's time - stopping ability with their own powers. Iron Man could try to create a device to counteract Dio's time stop, while Captain America uses his strategic skills to lead the fight against Dio's minions.
A great concept for a 'jojo persona crossover fanfiction' would be a tournament - style story. Characters from both universes are forced to participate in a battle royale. The Jojo characters would bring their Stands, and the Persona characters would have their Personas. The battles could be intense, with different strategies emerging. For instance, a Persona user might try to use psychological attacks against a Jojo character who is more used to physical combat with their Stand. And the story could also explore how the two groups of characters interact and form alliances outside of the battles.
Maybe there's a plot where a powerful and rare Pokemon is causing chaos in the Naruto world. The Naruto characters have to team up with some expert Pokemon trainers from the Pokemon world to stop it. Naruto could learn about the unique bond between trainers and Pokemon and apply some of those concepts to his relationships with his friends. And the Pokemon trainers could be in awe of the ninja techniques and use some of that knowledge to improve their own strategies.
A possible plot is that the Zoids themselves gain some of the abilities of Naruto characters. Imagine a Zoid being able to use chakra and perform ninjutsu. A Fire - type Zoid could use the Fireball Jutsu. This would completely change the dynamics of Zoids battles. Also, the story could revolve around a group of Naruto characters trying to stop an evil force in the Zoids world that is using Zoids in a way that could destroy both the Zoids world and the Naruto world. They would have to learn about Zoids and team up with local Zoid pilots to fight against this common enemy.
One idea could be a character from Naruto ending up in the Descendants' world. For example, Naruto himself could be transported there. He might use his ninja skills to deal with the challenges in the Descendants' world, like facing off against the villains in a very different way compared to the Descendants' characters. Maybe he'd use his shadow clone jutsu to confuse the bad guys or his Rasengan to take on powerful foes.
One idea could be that members of Root are sent to infiltrate the Hidden Leaf under the guise of being friendly shinobi. They cross paths with Naruto and his friends. Naruto, being the perceptive one, senses something off about them. This could lead to a series of battles and mind games as Naruto tries to expose their true motives.
Maybe there's a crossover where the Kyuubi's chakra has some strange effect on the Gargoyles. It could either enhance their powers in unexpected ways or cause some sort of chaos that they have to work together to fix. For example, the Kyuubi's chakra might accidentally awaken an ancient evil in the Gargoyles' world, and Naruto and the gargoyles must use their combined strength and wits to stop it.
Maybe in this crossover, Naruto has a vision of the Traveler from Destiny. Curious, he somehow manages to cross over to the Destiny universe. There, he meets the different classes of Guardians. He could learn about their weaponry and powers and in turn, teach them about chakra. They could then work together to stop a Vex invasion that is spreading across both universes.