It could be a rogue ninja who has a grudge against Sakura. This ninja might set her up in a way that makes her lose her license.
There's also the possibility that a new, powerful enemy from outside the village targets Sakura specifically. They manage to make it look like she's unfit to be a ninja, resulting in her losing her license, and they continue to be a threat as she tries to get it back.
Perhaps an elder in the ninja village who doesn't like Sakura's methods or her growing power. So they find an excuse to take away her license, making them the antagonist in this fanfiction.
It could be that she loses her license due to a mistake during a mission. Say she fails to protect an important artifact or person. As a result, she's stripped of her license. To get it back, she may have to train harder than ever, learn from her mistakes, and perhaps seek help from her friends and mentors. She'll need to show that she's now more reliable and capable to be a ninja again.
It could be Voldemort, even if he's already been defeated in the original story. His lingering influence might still haunt Harry. Maybe there are some dark magic remnants of Voldemort that keep causing problems and making Harry feel hopeless.
It could be Zuko if the fanfiction takes a different turn. Maybe Zuko, still struggling with his own inner demons, sees Aang's loss of control as an opportunity to take advantage and gain power. So he tries to manipulate the situation to his benefit.
It could be an old enemy like Kronos. Kronos is extremely powerful and cruel. He might target Percy's eye as a way to weaken him both physically and mentally. By taking away Percy's eye, Kronos hopes to make Percy less effective in battle and to shatter his confidence, which is crucial for leading the demigods against him.
It could be a new and powerful rogue ninja who manages to overpower Naruto and cause him to lose his arm. Maybe this antagonist has some sort of vendetta against Naruto or the Hidden Leaf village.
It could be a new dark wizard who has a vendetta against Harry. This wizard might have specifically targeted Harry's leg as a way to cripple him both physically and mentally. Maybe this antagonist has some sort of connection to Voldemort's old followers, seeking to finish what Voldemort started.
Perhaps Orochimaru. He might see Sakura's distraction from missing her chance as an opportunity to target Naruto or gain some advantage in his evil plans. He could manipulate the situation, making it even more difficult for Sakura to fix what she has missed.
Perhaps it could be a powerful ice spirit that has been awakened by some dark jutsu. This ice spirit has no concept of good or evil but is causing destruction as it spreads ice everywhere. Naruto and his friends would have to find a way to either seal it or make it understand the harm it's causing. In this case, the ice spirit would be the main antagonist as it opposes the well - being of the villages.
It could be Orochimaru. He's always been after power and new jutsu. If Naruto is guarding something really valuable, like a new powerful ninja technique, Orochimaru would be a likely antagonist. He'd stop at nothing to get his hands on it.
It could be Danzo. He was always a bit of a shadowy figure in the Naruto series. In a ninja tribunal fanfiction, he could be working behind the scenes to manipulate the tribunal for his own gains, perhaps trying to get rid of those who oppose his more extreme views on protecting the village.