You could also have a character who has a connection to both universes. Maybe a half - Naruto - half - Angeloid being. This character would act as a bridge between the two worlds. They would introduce the concepts of one universe to the other. For example, they could teach the ninja in Naruto's world about the advanced machinery of the Angeloid universe and at the same time show the Angeloid the importance of things like honor and loyalty in the ninja world. As this character moves between the two universes, the two start to blend together more and more.
In fanfiction, it could be that the technology of Gundam Seed Destiny is introduced into the Naruto world. The ninja villages could start using Gundam - like mechas in their battles. This would completely change the power balance. The shinobi would need to adapt to this new form of warfare. Also, the pilots from Gundam Seed Destiny could find themselves in the Naruto world and learn about chakra, and they might try to combine their piloting skills with chakra - based attacks.
One way could be through the concept of power. In Naruto, the Rinnegan gives extraordinary powers. In Game of Thrones, power is also a central theme. Maybe a character with the Rinnegan could be teleported into the Game of Thrones world and use their powers to vie for the Iron Throne. For example, they could use the Rinnegan's abilities to control minds, like the way the Red Woman in Game of Thrones uses her magic to influence people, but on a much larger scale.
One way could be through a powerful magic - ninjutsu hybrid spell. Maybe a character with knowledge of both worlds accidentally creates a portal that merges the two. For example, if a shinobi in Naruto world somehow gets hold of a magic item from Highschool DxD and activates it in a wrong way.
One way could be through a magical portal. Imagine in a fanfic, a powerful mage in the Game of Thrones world accidentally opens a portal to the Naruto universe. Dark Naruto, with his edgy and powerful nature, could be seen as a threat similar to some of the dark forces in Game of Thrones. He might form an alliance with a power - hungry lord in Westeros, thinking he can use their resources to achieve his own goals in the Naruto world. For example, if he teams up with Littlefinger, they could plot to take over both kingdoms using Dark Naruto's powers and Littlefinger's cunning.
One way could be through a magical or technological device. Maybe in the fanfiction, a character discovers an ancient artifact that can open portals between the Naruto universe and the Assassin's Creed Black Flag world. This device could be powered by chakra in the Naruto side and the Pieces of Eden from Assassin's Creed. Characters from both sides would then be able to cross over and interact, leading to all sorts of interesting scenarios like Naruto characters learning the ways of the Assassins or the pirates from Black Flag getting exposed to ninjutsu.
Another approach could be a shared enemy. Suppose there is an entity that exists in both universes in a different form. Writers could create a story where the characters from Highschool DxD and Prototype have to team up to defeat this entity. This would require them to understand each other's powers and work together, leading to a lot of character development and exciting action scenes.
Well, it might involve the political intrigue. The complex politics in Game of Thrones could be combined with the NERV organization's secrecy in Evangelion. Maybe the different houses in Game of Thrones are vying for control over the Evangelion units. And the pilots of Evangelion could be seen as pawns in this political game, just like many characters in Game of Thrones are used by the powerful lords.
One way could be through a powerful jutsu or hogyoku - like device. Maybe Naruto discovers a strange object that has the power to warp realities, similar to the hogyoku in the Bleach universe where Aizen Sousuke is from. This object could start to merge the two worlds, bringing the ninja world of Naruto and the Soul Society of Bleach together. As a result, Naruto and his friends would encounter Soul Reapers, hollows, and other Bleach elements, while the Soul Reapers would have to deal with the unique powers and politics of the ninja world.
In a Naruto x Star Wars Rebels fanfic, the two universes could be merged by exploring the idea of different cultures. The diverse cultures in Naruto, like the Hidden Villages, could be compared to the various planets and species in Star Wars. For instance, the Hidden Leaf Village could be seen as a planet in the Star Wars universe. The values and traditions of each could be shared. The Rebels' fight for freedom could be paralleled with the ninja's fight for their villages. This would allow for a deeper exploration of themes such as loyalty, friendship, and the struggle against oppression in both universes as the characters from Naruto and Star Wars Rebels interact and influence each other.
One way to merge them could be through character crossovers. For example, a character from Skyrim like the Dragonborn could find themselves in the world of Game of Thrones. They might use their unique abilities, such as Thu'um, to influence the power struggles in Westeros. Maybe they could form alliances with certain houses, or use their combat skills to fight in the battles there. Another aspect could be the introduction of Skyrim's magic system into the Game of Thrones universe. Spells like healing or firebolts could change the dynamics of warfare and politics in Westeros.