Perhaps the main antagonist could be a powerful wizard or sorcerer in the time the kid travels to. This character might be trying to manipulate the outcome of an important event for their own dark purposes, and the kid's attempts to ensure a 'win' go against their plans. Or it could be a corrupt official in a historical setting who doesn't want the underdog (the one the kid is helping) to win because it would disrupt their hold on power. The official then uses all their resources to stop the kid and those he's helping.
One possible antagonist could be an AI or advanced technological entity in a future world that the kid time travels to. The entity has been programmed to maintain a certain order in events, and the kid's actions to cause a 'win' for a particular side are seen as a disruption. It tries to outwit and stop the kid using its vast technological capabilities. Also, in a more fantasy - based time travel, it could be a demon or evil spirit that thrives on chaos and the 'loss' of the good side. The kid's efforts to create a win for the good guys are opposed by this malevolent being.
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.
It could be an alternate - version of Tony Stark from a different timeline who has gone rogue. This version might have different values due to the differences in his timeline's history and is now causing problems in the main Stark's timeline.
It could be a dark mage from the past who was sealed away but gets released because of Natsu's time travel. Maybe a mage who was trying to conquer the world back then and now sees Natsu as a threat to his new plans. Another option is a time - traveling villain who is trying to change history for his own evil purposes and Natsu has to stop him.
The main antagonist could be a virus that has infected the game's time - travel mechanism. This virus is spreading chaos throughout different time periods in the game world. It's trying to erase certain characters or events from history, and Ralph has to stop it. The virus could take on different forms in different time periods, making it very difficult for Ralph to combat.
A new, time - traveling villain could be introduced. This villain could be from a different dimension where time works differently. He comes to Ninjago to steal its time - related artifacts to power his own dimension. His unfamiliar powers and motives would make him an interesting and unpredictable antagonist.
Perhaps an alien race that has mastered time travel long before humans. They see Earth as a target for conquest, and they use time travel to disrupt history and weaken the planet's defenses. Peggy would have to figure out their plans and find a way to stop them. This would introduce an interesting sci - fi element to the fanfiction, with Peggy having to deal with advanced alien technology and culture.
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 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.
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.