One possible main antagonist could be a dark wizard from the past who senses Hermione's interference in the timeline and tries to stop her. This wizard might be afraid that Hermione's actions will change history in a way that will end his power or influence.
The main antagonists could be a group of time - traveling dark wizards who have their own malicious plans for the timeline. They see Hermione as a threat to their schemes and try to eliminate her. These dark wizards might be using time travel to gain more power, and Hermione's project gets in their way.
Perhaps the plot is centered around Hermione using time travel to save a loved one who was lost in a previous battle. She might have to navigate the complex rules of time travel, and along the way, discover secrets about the magic of time that no one knew before. This could lead to her having to make difficult choices between saving the past and protecting the present and future.
Bellatrix Lestrange could also be a common antagonist. She was extremely loyal to Voldemort and very powerful. If Harry and Hermione's actions in the past disrupt the Death Eaters' plans, she would surely oppose them.
There could be time - traveling dark wizards who oppose Harry and Hermione's attempts to fix things in the past. These wizards might have their own agendas for the past and present, and see Harry and Hermione as threats to their plans. They could use dark magic to try and stop them or even manipulate time against them.
It could be some of the historical villains from Naruto's past that were thought to be long gone but are now resurfacing due to the time travel. For example, Madara Uchiha might be an antagonist if they travel back to a time when he was still active and plotting against Konoha.
In some cases, time itself or the consequences of changing time could be seen as an antagonist. For example, if they try to change a major event, they might face unforeseen consequences like creating new threats or endangering the future they came from. So, in a sense, the very fabric of time and its rules could be working against them.
It really depends on the specific fanfiction. However, it could be that they travel back to a time when Orochimaru was at his most devious, so he would be a main antagonist. His experiments and thirst for power could pose a great threat to Naruto and Shikamaru's mission in the past.
Often, it could be the same antagonists from the original Naruto series but in a different context. For example, Orochimaru might still be an antagonist if he tries to use the time - travel situation to his advantage, like getting his hands on some ancient forbidden jutsu.
It might also be time itself. There could be some sort of time - related magic or force that doesn't want the past to be changed. So Harry and Tonks would have to face this 'antagonist' as they try to rewrite history. This could be in the form of time - locked spells or magical barriers that prevent them from interfering in certain events.
Often, Palpatine can still be a main antagonist even in time travel fanfiction. If Luke and Leia travel back in time, he might sense their presence and try to stop them from changing things that would undermine his power. Another could be Darth Vader if they travel to a time when he was still firmly on the dark side. He would be a powerful foe for them to face.
Often, it could be dark wizards from the past who oppose Harry and Amelia's attempts to change things for the better. For instance, a dark wizard who wants to keep a certain evil spell in place that Harry and Amelia are trying to stop.