One common theme is the clash of cultures. Naruto's ninja world has its own set of values and abilities, and the Assassin's Creed world has its own lore and rules. Another theme is power - how Naruto's 'godlike' powers change the power balance in the Assassin's Creed world.
One popular 'godlike Naruto Assassin's Creed crossover fanfiction' might be found on platforms like FanFiction.net. You can search there using relevant tags. There are often stories where Naruto's abilities are combined with the Assassin's Creed world in really creative ways.
One possible plot could be that Naruto, with his ninja skills, gets transported to the Assassin Creed world. He might team up with an Assassin, perhaps Ezio. Together, they could use Naruto's chakra - based attacks and the Assassin's stealth and combat skills to take on a common enemy, like a powerful Templar - like figure who is threatening both the ninja world and the Assassin's world.
A cool plot could be that the Templars in the Assassin's Creed world somehow get hold of some ninjutsu scrolls. They start using these to create an army of super - soldiers. The Naruto characters then team up with the assassins to stop the Templars. Naruto could use his Rasengan against the Templars' new warriors, while Altair could use his eagle vision to spot their weaknesses. Together, they could form a unique combat strategy that combines the best of both worlds.
One possibility could be a story where Naruto is somehow transported to the world of Assassin's Creed Black Flag. He might use his ninja skills to adapt to the pirate - filled environment. For example, his ability to run on water could be seen as a superhuman feat among the pirates and assassins.
Well, it could have Naruto characters using Assassin's Creed skills like parkour. For example, Naruto could be running across the rooftops of Konoha in the same fluid way as an Assassin. Maybe Sasuke would be like an assassin with his stealth and quick strikes.
The plot could involve Naruto characters in the Assassin's Creed world. Maybe Naruto himself could be an assassin with his ninja skills. He'd be sneaking around ancient cities, using his shadow clones to distract guards just like assassins use decoys. It would be really cool to see him climb buildings and assassinate targets in a more historical and different setting than the ninja villages.
I think Naruto would be the most interesting. His energetic and determined personality would make for great stories in the Assassin's Creed world. He'd be constantly trying to adapt and use his ninja skills in new ways. His ability to make friends and inspire others would also lead to some interesting interactions with the assassins.
I think Sasuke would be quite interesting. His dark past and thirst for power could be paralleled with some of the Assassin's Creed characters' motives. He could learn new ways to use his skills in the Assassin's Creed world and maybe even find a new purpose.
I think Naruto and Altair would make an interesting pair. Naruto is all about exuberance and his belief in the power of friendship and hard work. Altair, on the other hand, is a more stoic and methodical Assassin. Their different personalities would create great character dynamics. Naruto could learn about Altair's strict code of conduct and Altair could be intrigued by Naruto's ability to keep going no matter how tough the situation is.