Maybe a rogue ninja from Naruto's world who has also found his way into Negima's world. He is jealous of Naruto's popularity among the students in Negima and decides to be the antagonist. He could try to break Naruto's seals and cause chaos in the new world.
It could be an evil wizard from Negima's world who wants to use Naruto's power for his own dark purposes. This wizard might be aware of Naruto's unique sealing abilities and see it as a way to gain ultimate power over both the ninja and magical worlds.
It could be one of the dark mages from the Mahou Negima Sensei world who sees Naruto as an intruder and a threat to their plans. Maybe they want to steal his chakra for their own dark magic purposes.
A really interesting plot could be a time - travel scenario in the 'Naruto Sealed Negima' fanfiction. Naruto is sealed and sent back in time to the world of Negima. He then has to use his skills and knowledge from his own time to survive in this new world. He might become a teacher or mentor to the young students in Negima, teaching them some of his ninja techniques while also learning about magic from them.
Maybe it's an ancient evil that was sealed away long before Naruto but managed to break free during his 1000 - year imprisonment. This evil entity now wants to destroy the world and sees Naruto as an obstacle once he is unsealed.
It could be Orochimaru. He has always been interested in power and Naruto's unique abilities. With Naruto sealed away, Orochimaru might see it as a chance to steal whatever power Naruto had or use his absence to further his own evil plans in the ninja world.
A corrupt leader from a political - based crossover world might be the main antagonist. He views Naruto as a threat to his power, especially with the mystery of his seal. So, he tries to either keep Naruto sealed away permanently or use the situation to gain more control over his own people by creating fear around Naruto's presence in their world.
Perhaps an old enemy has returned, stronger than ever. They might have been plotting during Naruto's sealing and now are ready to take on Naruto and the Hidden Leaf Village. This could be someone like Orochimaru who found a new way to gain power in Naruto's absence.
The main antagonist could be a new character created specifically for the fanfiction. This character might be from a long - lost clan that has a grudge against the Uzumaki clan, of which Naruto is a part. Since Naruto is the last of the Uzumaki in the village, sealing him away would be their first step in getting revenge on the clan, and they would do everything in their power to keep him sealed.
Another possibility is a character who has been corrupted by the same power that was used to seal Naruto. This character could see Naruto's awakening as a threat to their new - found power or status. For example, if the sealing was related to some ancient and dark chakra, a ninja who has been influenced by this chakra might oppose Naruto.
It could be someone from the Naruto universe who doesn't like Naruto's newfound fascination with Aku. For example, Danzo might see Naruto's interest in Aku as a threat to the stability of the village and try to stop Naruto from further exploring Aku - related things. So, Danzo could be the main antagonist in this case.
Maybe a new character could be introduced as the main antagonist. This character could be from a hidden village that has been secretly observing Naruto's growth. They realize his potential as a weapon and plan to steal his power or use him to start a war against other villages.