One possible plot could be that Naruto and his friends from the Naruto universe are suddenly transported to the Destiny universe. They could be mistaken for new Guardians at the Tower. Naruto's chakra abilities might be misinterpreted as a new form of Light power. They then have to team up with Destiny's Guardians to fight against a common enemy that threatens both universes, like a powerful Darkness entity that has somehow found a way to cross over from Naruto's world where the Akatsuki's actions have weakened the barriers between worlds.
For me, it would be the Nine - Tails from Naruto. Imagining how the giant, powerful fox would be perceived in the Destiny universe, where there are all kinds of strange and powerful creatures, would be really cool. And from Destiny, the Exo Stranger. Her mysterious nature and time - traveling abilities could add a lot of intrigue to the crossover. Another interesting character to focus on could be Sakura. Her growth as a medical ninja and her combat skills could be useful in the Destiny setting, and her relationship with Naruto and Sasuke could bring in some interesting character dynamics.
One idea could be to cross Naruto with another popular anime like One Piece. Naruto characters could end up on the Grand Line, facing pirates and searching for the One Piece while using their ninja skills. Another idea is to cross it with a fantasy series like Harry Potter. Picture Naruto and his friends attending Hogwarts and learning magic alongside their ninja training. Or perhaps a crossover with the DC Universe, where Naruto characters gain superpowers similar to the DC heroes and fight against villains in a new, urban setting.
Power adaptation is also a theme. Naruto has his chakra-based powers, while Destiny has a wide range of powers like the use of Light and Dark, and different weapon types. In these fanfictions, Naruto usually has to figure out how to use or adapt to these new powers. For example, he might try to combine his Rasengan with the energy blasts in Destiny. And there's often the theme of heroism. Both Naruto and the characters in Destiny are often in situations where they need to be heroes, so in the fanfiction, it's about how Naruto fits into that hero - centric world of Destiny and vice versa.
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.
If it's a Naruto and One Piece crossover, Naruto and Luffy could make a great pairing. They both have strong leadership qualities and a determination to achieve their goals. In a Naruto - Harry Potter crossover, Naruto and Hermione could be an interesting pair. Naruto's action - oriented nature combined with Hermione's intelligence would lead to some great adventures. For a Naruto - DC crossover, Naruto and Superman could be paired. Superman's powers and Naruto's ninja skills could make for a formidable team against powerful villains.
A third idea could be a crossover where some of the Destiny characters end up in the Naruto universe. They would have to learn how to use chakra and ninjutsu. The Guardians could be amazed by the different fighting styles in Naruto's world. And they could also share their knowledge of advanced weaponry and space - time manipulation with the ninjas, leading to some really unique battles and alliances.
Naruto and Cayde - 6 would be an interesting pairing. Naruto's energetic and positive personality would contrast with Cayde - 6's sarcastic and somewhat reckless nature. They could learn from each other, like Naruto teaching Cayde - 6 about the importance of friendship and never giving up, while Cayde - 6 could show Naruto some of his cool gadgets and weapons.
Another challenge is creating a plot that makes sense for both sets of fans. The story has to appeal to Destiny 2 fans as well as fans of the other game. If it's too focused on one side, the other group of fans might not enjoy it. For instance, if a crossover with The Elder Scrolls is too centered on Destiny 2 mechanics and doesn't incorporate enough of The Elder Scrolls' rich world - building, it could be a turn - off for Elder Scrolls fans.
One idea could be that Jinx somehow gets transported to the Naruto universe. She might initially be seen as a strange and powerful figure. Naruto, being the curious and friendly type, would approach her. Jinx could then start causing chaos in the Hidden Leaf Village, which Naruto has to deal with while also trying to understand her. And they could gradually form an unlikely friendship as they learn from each other's worlds.