Another theme is power and control. In the Matrix, there's the idea of the machines controlling everything, while in Naruto, there are different power structures like the ninja villages. When these two worlds cross over, the theme of who has power and how it's controlled becomes very interesting. For example, how would the ninja deal with the all - powerful machines of the Matrix?
The plot could start with Naruto and his friends somehow being pulled into the Matrix world. They initially mistake it for a powerful genjutsu. As they explore, they meet Neo and the other rebels. They realize that the Matrix is a different kind of prison compared to the world they know. Naruto decides to help the rebels fight the Machines, using his ninja skills. Meanwhile, the agents in the Matrix see Naruto and his friends as a new threat and start devising ways to stop them.
A different approach could be that characters from the Matrix world are brought into the Naruto universe. Trinity could learn some ninja techniques from the Konoha ninja. The Matrix characters would be amazed at the concept of chakra and how it can be used for various powers, like walking on walls or creating fireballs.
It could work if we consider the power systems. The Matrix has the power of the One, who can manipulate the code of the Matrix. In Naruto, there are jinchuriki like Naruto who have great power. If Naruto were to enter the Matrix, his chakra and the Nine - Tails' power could potentially interact with the Matrix's code. He might be able to break through the digital barriers or even rewrite parts of the Matrix code with his chakra, just like how he can use his chakra to perform powerful jutsu in his own world.
He would likely retain his sense of justice. In the Matrix, he might see the oppression by the machines as something similar to the problems in his own world. So he'd want to fight for the freedom of the people trapped in the Matrix. His character would also adapt to the digital environment. For instance, he might use his chakra to enhance his speed and strength in a different way than in his normal ninja world, like using it to boost his reaction time against the fast - moving digital threats.
In a Naruto in the Matrix crossover fanfiction, Naruto would bring his own values of friendship and loyalty. He'd be shocked at first by the lack of real nature in the Matrix. His training as a ninja would give him an edge in combat within the Matrix. However, he'd also have to learn about the Matrix's rules. Maybe he'd start by trying to find a way to use his chakra to hack into the system, much like Neo learned to manipulate the Matrix code.
Most likely, characters from 'The Hobbit' like Bilbo Baggins and Gandalf would be main characters. They would be the ones interacting with elements of the Matrix world.
In this fanfiction, Skynet could find a way to connect to the Matrix. It might try to take over the Matrix and use it to control more humans. The machines in the Matrix might initially resist, but Skynet could offer them a deal to share power over humanity.
One common theme is power struggle. Since Smith is a powerful character in the Matrix, when crossed over, there's often a battle for dominance. Another theme could be identity crisis. Smith might have to adapt to a new world or set of rules in the crossover, which challenges his sense of self.
Adventure is also a big theme. The characters embark on new quests in unfamiliar settings. For instance, if Naruto is in the Mushroom Kingdom, he has to figure out how to deal with Goombas and Koopas while still maintaining his ninja skills. And for Mario in the Hidden Leaf, he has to adapt to the more dangerous and stealth - based ninja world. There's also the theme of power, as they combine their unique powers to face challenges.
Friendship and cooperation are big themes. Naruto, being a character who values friendship highly, forms bonds with witches in these crossovers. They have to learn to trust each other despite their differences. Also, identity is a theme. Witches may have to hide their true identities in the Naruto world, and Naruto characters might question their own identities when exposed to the new and strange world of witches.