One common theme is the struggle for identity. Many bad guys in Naruto fanfiction are not just pure evil. They have a backstory that makes them question who they are. Take Zabuza for instance. In some fanfics, his life as a rogue ninja is explored more deeply, and he's constantly fighting between his identity as a killer and his possible redemption. Another theme is the misuse of knowledge. Characters like Kabuto use their medical knowledge in a bad way. And of course, there's the theme of isolation. Bad guys often isolate themselves from the rest of the ninja world, either by choice or because they are shunned, which then further fuels their villainous actions.
Power - hunger is a common theme. Bad guys in Naruto often seek more power, like Orochimaru always hunting for new jutsu and ways to be immortal. Another theme is revenge. For example, Sasuke's journey towards vengeance against Itachi was a big part of his villain - like arc in some fanfictions. Also, the idea of chaos and disrupting the established ninja order is often there, as seen with characters like Pain who wanted to make the world feel the pain to create a new order.
One common theme is Guy's dedication to his ninja way. Fanfictions often highlight how he never gives up, no matter the odds. Another theme is his relationship with his students. For example, how he trains and mentors them. Also, his rivalry with Kakashi is a frequent theme, showing their friendly competition and mutual respect.
Manipulation. Bad guys often manipulate others in the name of love. For example, they might lie to get closer to someone they desire.
Common themes might include the blurring of the lines between friendship and romance. Given that Naruto is now on Team Guy in a yaoi fanfiction, the characters would likely experience a shift in how they view each other. There could be themes of loyalty being tested in a different way, as romantic feelings enter the picture. Also, the theme of personal growth through these new relationships is likely. For example, Naruto might learn different values from Team Guy members while also exploring his own emotions in a more homoerotic relationship.
Redemption is a very common theme. The bad guy realizes the error of their ways and tries to make up for their past misdeeds. Another theme is the power of love or friendship. For example, like in 'Despicable Me' where Gru's relationship with the girls changes him. Also, self - discovery is often involved. The bad guy discovers a better part of themselves that was hidden under their villainy.
Forgiveness is a common theme. The good - hearted person in the relationship often has to forgive the bad guy for his past wrongdoings. For example, in 'Beauty and the Beast', Belle has to overlook the Beast's initial rudeness.
Sacrifice. The 'bad guy' turned good often has to make sacrifices in the name of love. In 'Titanic', Jack, who was a bit of a scoundrel in some ways at the start, falls in love with Rose. In the end, he sacrifices his life for her, which is also a form of redemption as he goes from a carefree character to one who shows ultimate self - lessness.
One common theme is justice. The good guy is usually fighting for what is right and fair, like in a story where a detective (the good guy) chases a criminal (the bad guy) to make sure the law is upheld. Another theme is sacrifice. Sometimes the good guy has to give up something to defeat the bad guy, for example, a hero leaving his family to go on a dangerous journey to stop an evil force. Also, redemption can be a theme. Maybe the bad guy has a chance to change in the story, but often they don't take it and the good guy has to force the situation to a conclusion.
One common theme is isolation. Since Naruto had a bad childhood, fanfictions often focus on how he was alone as a child. Another theme is the search for identity. He didn't have his parents, so he's constantly trying to figure out who he is in these stories. And revenge can also be a theme. Some fanfictions might explore if Naruto would seek revenge against those who made his childhood miserable.
Friendship is a common theme. The three characters often form a strong bond, like in a story where they grow up together in a small town. They support each other through different life events, whether it's a family issue for one of them or problems at school.
A third common theme could be loyalty. How they are loyal to each other and to their friends. Fanfictions often test this loyalty in different situations, like when they are faced with difficult choices that could affect their relationships.