A new character created specifically for this fanfiction could be the main antagonist. This character could be a powerful being that has been awakened by the presence of Link from Ocarina of Time in the World of Light. This new villain could be jealous of Link's power and the attention he gets from the other characters in the World of Light and thus seek to destroy him.
Ganondorf would be an obvious choice. Since he is the main villain in Ocarina of Time, he could continue his reign of terror in the World of Light. He might even gain new powers or form alliances with other dark forces in this new world.
It could be Ganondorf. Since he is the main antagonist in The Legend of Zelda: Ocarina of Time, it's likely that he would also be the main foe in this fanfiction. He would be a great challenge for Yugi as he has a lot of dark magic and power.
It could be a new villain who has risen to power during Naruto's absence. This villain might have a vendetta against Konoha or the ninja world in general because of something that happened while Naruto was away.
It could be a rogue ninja who has made a pact with the demons in the demon world. This ninja has turned against the ninja world and wants to use the power of the demon world to rule over all. He would constantly oppose Naruto's attempts to restore peace.
Perhaps a group of elite warriors in the new world who are jealous of Naruto's unique abilities. They form an alliance to take him down because they fear he will disrupt their status quo and take over their positions of power.
It could be a powerful kunoichi who opposes Naruto's presence in her world. Maybe she sees him as a threat to the existing power balance among kunoichi.
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 an ancient evil ninja who was sealed away long ago and somehow gets released in the time chamber. Naruto has to face this powerful foe while also dealing with the time - warped environment of the chamber.
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.
Cell could be a great antagonist. Even if Gohan goes back in time, Cell might still find a way to exist. Maybe he adapts his plan to absorb the Androids earlier in time. Gohan would then have to face a more powerful and unpredictable Cell, who could potentially change the timeline to his own advantage.
Frieza would be a great antagonist. If Goku goes back in time to a point before Frieza was defeated, Frieza could be an even more menacing force as Goku might not have all the power - ups he had in the original timeline. He'd have to rely on his wits and basic training more.