Madara Uchiha could be a great antagonist. Imagine if the Third Hokage travels back to a time when Madara was still alive. Madara, with his grand plans for the ninja world, would see the Third Hokage as an obstacle. He might try to use the time - traveling Hokage to his own ends, or simply try to eliminate him to ensure his own vision for the world comes to pass.
Another option could be a rogue ninja from the future who has somehow managed to time travel. This ninja could be disgruntled with how the Third Hokage ran Konoha in the future. So, he travels back in time to try and take over the village or at least disrupt the Hokage's rule. He might have some new and dangerous jutsu that the Third Hokage has never seen before, making him a formidable foe.
It could be an older version of Orochimaru who has also found a way to time travel. He might try to change the past to his advantage, like getting rid of the Third Hokage before he can become a threat to his future plans. Orochimaru is always power - hungry and his older self could be even more dangerous with knowledge of the future.
It could be someone who wants to expose Naruto's secret. Maybe a rogue ninja who wants to use this information to create chaos in the village by making the villagers doubt Naruto's intentions.
A group of rogue ninjas from other clans who oppose the idea of the Hidden Leaf Village. They see the Shodai Hokage's leadership as a threat to their own power and freedom. They might team up and use underhanded tactics like assassinations, sabotage of the village's resources, and spreading false rumors to try and undermine the Shodai Hokage's authority. They could also form alliances with other enemies of the village, making them a formidable and complex antagonist group.
It could be a rogue ninja who was once a part of the Akatsuki but managed to escape before their downfall. He's been biding his time, growing stronger, and now he wants to take revenge on Naruto and the Hidden Leaf for what happened to the Akatsuki.
It could be a rogue ninja who was once a part of Konoha but was banished for unethical experiments. Now, with a thirst for revenge against Naruto and the village, he returns as a powerful and unpredictable foe.
It could be a time - traveling sorcerer who wants to change history for his own evil purposes and sees Achilles as a threat. The sorcerer might try to stop Achilles from getting back to his own time or use his knowledge of the future to his advantage against Achilles.
Perhaps an ancient evil that was sealed away long ago but is released due to Temari's time - traveling disruptions. This evil entity then starts causing chaos in the past, and Temari is the only one who can stop it with her modern skills and knowledge.
A time - traveling bounty hunter could be the main antagonist. He might be after Lucy because she has somehow disrupted the time - space continuum. He's cold - hearted and will stop at nothing to bring her to some time - traveling justice.
Cell could be a great antagonist. Imagine Goten travels back in time to before Cell was complete. Cell could sense Goten's power and try to absorb him to become even more powerful. This would put Goten in a tough situation where he has to avoid Cell while also trying not to disrupt the timeline too much.
It could be a time - traveling villain who is trying to disrupt the timeline for their own gain. This villain might be trying to erase certain events or people from history to change the future in a way that benefits them.
It could be a time - traveling villain from the future who wants to change the past to gain more power in their own time. They might try to stop Naruino from achieving their time - travel goals.