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.
A great plot could involve a group of ninjas from the Naruto world being accidentally teleported to the Tower in Destiny. The Guardians are initially suspicious but then realize that they share a common enemy. The ninjas' stealth and jutsu could be used to infiltrate enemy bases in Destiny, while the Guardians' long - range attacks and super abilities would be useful in open battles in the Naruto world.
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.
One idea could be that the characters from RWBY are transported into the Destiny universe and have to learn to use the unique weapons and powers there. For example, Ruby could be fascinated by the Exotic weapons in Destiny and try to incorporate their technology into her Crescent Rose. Another plot could involve the Guardians from Destiny being sent to the RWBY world to help fight against the Grimm. They would have to adapt to the new environment and team up with the RWBY characters. The third idea is that a powerful enemy from the Destiny universe somehow crosses over to RWBY's world and the combined forces of both universes have to stop it.
Perhaps the Voldemort threat in the Harry Potter world is somehow connected to a Darkness - like entity in Destiny. Harry and his friends must learn new combat techniques from the Guardians or other Destiny characters to combat this new, more powerful form of the Dark Lord. They could also exchange magical and technological knowledge, which would be really cool to see.
One idea could be a group of Guardians from Destiny being transported to the Star Wars universe. They could team up with the Jedi to fight against the Sith and the Darkness that threatens both universes. Maybe they would introduce their advanced weaponry and abilities to the Star Wars characters.
Another plot could involve a shared enemy that exists in both universes. The combined forces of Mass Effect races and Destiny Guardians have to figure out how to defeat this enemy. They would need to overcome their differences in culture and combat styles to be successful.
One idea could be a crossover with another mecha anime like Macross. The characters from Gundam Seed Destiny could find themselves in the middle of a space battle in the Macross universe, having to adapt to the different technology and combat styles. For example, they might encounter the transforming Valkyrie mechs and have to figure out how to fight against them or even team up with the Macross pilots.
One interesting plot idea could be a crossover where Naruto characters enter the Hunter x Hunter world and have to adapt to its unique nen abilities. For example, Naruto might try to use his chakra in new ways to mimic nen techniques.
One idea could be that the Master Chief from Halo is transported to the Destiny universe and has to team up with a Guardian to stop a new threat that is using technology from both universes. For example, the Covenant and the Fallen might be working together under a powerful new leader.
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.
Imagine if the main characters from both universes swap places. Naruto finds himself in the Gundam Seed Destiny world, having to pilot a mobile suit and fight in a war he doesn't fully understand. Meanwhile, a Gundam pilot like Kira Yamato ends up in the Naruto world, having to learn about chakra and become a ninja. They both have to adapt to their new surroundings and use their unique skills to survive. This would allow for a lot of character development as they face new challenges and make new friends (or enemies) in their respective new worlds.