A common theme is the clash and then the fusion of different power systems. Naruto's chakra - based ninja skills and the magic from the other universe, like spells in Harry Potter or magic in Fairy Tail, often start by being at odds but then find a way to work together.
Conflict is also a big theme. There could be conflict between those who use traditional ninja skills and those who start using magic. For example, some may see magic as a threat to the established ninja order. And there's often a theme of self - discovery too. As the character uses magic, they learn more about themselves and their place in the world.
Another theme is the discovery of hidden chakra abilities. Many fanfictions revolve around a character finding out they have a special form of chakra that can be used as magic. This could be something like a chakra that can heal in extraordinary ways or one that can manipulate time on a small scale. In these stories, the characters then have to learn to control and use this new - found power. It often leads to them having to face challenges both from within their own community who might be jealous or afraid of their power, and from external enemies who want to use their power for their own evil purposes.
One common theme is power acquisition. Since there's a 'god of magic', characters often seek to gain power from this new magical source. Another is the clash between the traditional ninja world and the new magical elements. It can also involve themes of redemption, as characters might use the new magic to atone for past mistakes.
Friendship is a very common theme. Since it's about Naruto and his friends in a crossover, it often shows how their bonds are strengthened or tested in the new situations. For example, they might have to rely on each other more than ever.
A common theme is the clash of cultures. Naruto's ninja culture from his world is very different from the military - and magic - based culture in 'The Gate'. So, exploring how these two cultures interact is often seen. For example, Naruto might introduce the concept of chakra to the people of 'The Gate' world.
Character growth is also a major theme. In a long 'Naruto' crossover fanfiction, Naruto usually has to face new challenges in the crossed - over world. This forces him to adapt and grow in ways he didn't in his original 'Naruto' world. For instance, in a crossover with the 'Fullmetal Alchemist' world, he has to learn about alchemy and its rules, which broadens his understanding and skills.
One common theme is power. The shinju is a powerful entity, and when crossed over with Naruto, it often involves the characters either seeking its power or having to deal with the consequences of its power. For example, in many fics, Naruto might be tempted by the shinju's power to achieve his goals more quickly.
A major theme in these fanfictions is identity struggle. Naruto, being in a chaotic crossover, may question who he is and how he fits into this new, disordered world. Also, the theme of friendship and alliances is quite common. He has to form new alliances with characters from the chaotic world, and these relationships are explored in depth. For instance, he might team up with a chaotic being who has different motives, and they have to work together despite their differences.
One common theme is redemption. Naruto, being banished, often has to prove himself all over again in the new crossovers, seeking redemption for whatever led to his banishment in the first place.
One common theme is the idea of over - coming adversity. Since Naruto is blind, he has to find ways to be as strong or even stronger than he was before. Another theme could be the discovery of new powers or abilities that compensate for his blindness.