Maybe an envious noble who is jealous of the attention and influence Sakura gains in the warring era. This noble might spread false rumors about her, try to frame her for crimes, and generally make her life difficult. He could also try to form alliances against her with other nobles who are threatened by her presence.
It could be a dark sorcerer who has been secretly manipulating the warring factions from the shadows. When Sakura arrives, he senses that she has the potential to expose him and stop his evil schemes, so he becomes her enemy. He might use dark magic to try and thwart her efforts to bring peace or stability to the era.
A power - hungry warlord who sees Sakura as a threat to his plans of total domination could be the main antagonist. He might fear that her knowledge or the changes she brings could disrupt his hold on power, so he tries to eliminate her at every turn.
Maybe an ancient evil spirit that has been awakened by the bloodshed of the Warring States period. It starts to possess the warlords and turn them against each other, and Sakura has to find a way to exorcise the spirit before it destroys everything. In this case, the spirit is the main antagonist as it is the root cause of the chaos.
One interesting character could be a powerful warlord. The contrast between Sakura's modern sensibilities and the warlord's traditional, often harsh, leadership style would create a lot of tension and potential for character development. Another could be a mysterious healer. Sakura could learn from the healer's ancient medical knowledge, and they could form a bond over helping the wounded in the war - torn land. A young and idealistic warrior who is new to the ways of war could also be a great pairing. Sakura could inspire the warrior with her modern ideas of peace and justice.
One plot idea could be Sakura traveling back to the warring era and using her modern medical knowledge to save the lives of many soldiers. This would not only change the course of small battles but also gain her the respect and protection of different warring factions.
A time - traveling pirate who has his own agenda and wants to change the course of pirate history for his own gain could be the antagonist. This pirate might be jealous of Luffy's future achievements and try to stop him from ever becoming the Pirate King by changing things in the past.
The Riddler could be a great main antagonist. He could use his knowledge of time paradoxes and puzzles to try and outwit Batman as he travels through time. He might set up elaborate traps across different time periods that Batman has to solve.
The main conflict could be Naruto's struggle to fit into the very different social and cultural norms of the Warring Clan Era. As a time - traveler, she has modern ideas and values that might clash with the more traditional and clan - centric views of that time.
Maybe the main antagonist is an evil organization that has been secretly infiltrating the village. They target Sakura because of her skills and knowledge. They deceive her into believing that her village is the real enemy, causing her to betray her comrades.
It could be a future version of an existing villain who has also found a way to time - travel. For example, a more powerful and cunning Orochimaru from a future timeline where he has mastered even more dark jutsu. He might try to stop Naruto from changing the past in ways that would prevent his own rise to power.
It could be a dark wizard from the past who somehow senses that Harry and Teddy don't belong in that time and tries to use their presence for his own evil gains. Maybe he wants to steal their future knowledge to become even more powerful.
There's also the possibility that the main antagonist is an outside force from another dimension or a powerful entity that was awakened in the future. This entity might see the ninja world as a threat or simply want to conquer it for its own gain. Naruto would need to figure out how to defeat this unknown and powerful foe during his time in the future.