Perhaps a dark spirit or a demon. It could lurk in the shadows, waiting for the right moment to strike fear into Sakura. Its otherworldly powers and appearance would be so terrifying that it causes her to be scared pee.
A powerful and evil ninja could be the antagonist. He could be after Sakura for some secret knowledge she has. His menacing presence and attacks could be what scares Sakura so much that she has the accident.
It could be that Sakura is in a dark alley at night. A group of mysterious figures start to surround her. The sense of danger terrifies her and she pees in fear. She then has to think quickly, like using some of her medical knowledge to create a distraction and run away.
In this fanfiction, the main antagonist could be a strict teacher. Sakura, being a boy with a free - spirited nature, often clashes with the teacher's rigid rules. The teacher always seems to be out to get Sakura, giving him unfair punishments and trying to suppress his creativity or individuality.
A rogue shinobi who has a personal vendetta against Sakura or her friends. Maybe this shinobi blames Sakura for something that happened in the past and decides to kidnap her as revenge. He could be a powerful and unpredictable antagonist.
It could be a powerful dark wizard who wants to use Sakura's powers for his own evil purposes. He might be constantly trying to capture her or manipulate her into doing his bidding.
Another potential antagonist could be an enemy that Orochimaru and Sakura face together during her training. This enemy might have a vendetta against Orochimaru and see Sakura as an extension of him. So while Orochimaru is training Sakura, this new enemy could be the one causing the most immediate problems and danger for them both.
Another option is a jealous individual from Sakura's own time who somehow manages to follow her into the past. This person is envious of Sakura and wants to take over her role in the past - time events. They would constantly try to undermine Sakura and take credit for her actions, causing a lot of trouble for her during her time - traveling adventure.
A rogue ninja who wants to steal the power of the contract for his own evil purposes could be the main antagonist. He might be jealous of the connection between Sakura and Itachi and wants to break it to gain the abilities they could potentially unlock together.
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.
It could be Orochimaru. Since he has always been interested in powerful ninja abilities, he might see Sakura with the Sharingan as a new target. He could try to steal the Sharingan from her to add to his own collection of powerful jutsus and abilities.
It could be a time - traveling villain who doesn't want Sakura to succeed in her journey in the future. This villain might be from Sakura's own time but has different motives in the future setting.