Kaguya Otsutsuki could also be a main villain. If Naruto travels to a different time period, he might accidentally release Kaguya or she could sense his Rinnegan power from afar and see him as a threat. She could then try to stop Naruto from changing the future or past in a way that would prevent her from being resurrected or stop her plans.
Well, when it comes to Naruto time travel and Rinnegan in fanfics, it's often about exploring new storylines. Maybe Naruto himself gets the Rinnegan and travels back in time to train his younger self. This would make him a much more powerful ninja at an earlier stage and could completely change the power balance in the Hidden Leaf Village and among the other ninja villages as well.
Darkseid could be the main villain. Imagine Darkseid learning of Superman's ability to time - travel and using it to his advantage. He could try to invade different time periods to gain more power and resources. Superman would have to fight him across time and space to protect all of existence.
The Emperor could still be a main villain even in a Padme time travel fanfiction. If Padme travels to a time when the Emperor is already in power, he would surely oppose her as she represents a threat to his rule. He might try to manipulate events to keep her from changing the future or past, depending on where she travels to.
Madara Uchiha might be the main villain. He has powerful time - related abilities in the original series. He could use his Mangekyo Sharingan or other powers to freeze Naruto in time. His goal could be to disrupt the balance of power in the ninja world. With Naruto out of the picture, he can more easily carry out his plans to reshape the world according to his own vision. He might see Naruto as a major obstacle to his grand plan, so he freezes him to eliminate the threat.
Well, in this fanfiction scenario, perhaps Naruto's Rinnegan gives him unique abilities during the time travel. He and Anko could team up to take on threats that were previously unbeatable. They might also discover secrets about the origin of the Rinnegan or other powerful jutsus that were lost in time. It could be a story of self - discovery for both of them as they navigate a different era.
The main villain could be a time - traveling version of one of his regular foes, like Slade. Maybe Slade from the future has developed a way to manipulate time and he's going back in time to stop Beast Boy from ever becoming a Titan or to change events in his past that will make him easier to defeat. Another option could be an ancient evil that was sealed away in the past and Beast Boy's time travel accidentally releases it. It then tries to take over the present by changing key events in history. And it could also be a future version of Beast Boy himself who has been corrupted by power and is trying to change the past to make himself even more powerful.
The Rinnegan can be used in time travel fanfiction in Naruto in various ways. It could be used to open portals to different time periods, kind of like how it can create spatial portals in the original series. For example, a character might use the Rinnegan to travel back to the era of the First Hokage to gain knowledge or power.
There's also 'Naruto's Time - Traveling Rinnegan Adventure'. This fanfiction focuses on Naruto exploring different time periods with his Rinnegan ability. He meets his predecessors and learns a great deal about the origin of the ninja arts. It's a great read for those who love to see Naruto in a more introspective and knowledge - seeking role as he travels through time.
One possibility is that Naruto with his Rinnegan powers could disrupt the power balance in the Sannin era. His modern jutsu and knowledge might give him an edge. For example, he could use his Rasengan in ways that the shinobi of that time have never seen. He might also form unexpected alliances, like befriending Orochimaru before he goes bad, which could change the entire future of the Naruto world.
Well, one possibility is that Naruto with the Rinnegan could use his newfound power to protect Kushina during their time travel. Maybe he can prevent some of the tragedies that happened in the past. For example, he could stop the Nine - Tails attack on the village by controlling the beast in a more efficient way with his Rinnegan powers.