Sometimes, it might be the forces that oppose the changes Naruto and Tsunade are trying to make in the past. These could be ninja from different villages who don't want the power balance to be disrupted. There could also be ancient evils or powerful ninja from the past who see Naruto and Tsunade as threats to their way of life or their own power - seeking plans.
In some fanfictions, the main antagonists could be time - altered versions of characters. For instance, if a character who was originally good in the present timeline gets corrupted in the past due to some unforeseen circumstances caused by Naruto and Tsunade's time travel. It could also be a new group that rises to oppose them as they try to change the course of history.
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.
Often, Orochimaru can still be a main antagonist. Even in a time - travel scenario, his thirst for power and immortality doesn't change. He might oppose Naruto and Tsunade's attempts to change the past as it could disrupt his own plans for power.
It could be a group of rogue ninjas who also ended up on the island. They might be after some valuable resource on the island and see Naruto and Tsunade as obstacles.
It could be a group of rogue ninjas who want to steal Naruto's godlike powers for themselves. They might be led by a powerful and evil ninja who has his own motives for wanting such power.
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.
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.
It could be the same antagonists from the original Naruto series, like Orochimaru or Madara Uchiha. Since Naruto and Temari are time - traveling, they might encounter a younger version of these villains at a time when they were just starting their evil plans. Another possibility is that they create new antagonists by changing the past in some way. For example, if they prevent a certain character from dying, that character could turn out to be an antagonist in the altered timeline.
In some versions, Orochimaru could be a main antagonist. Since he has his own devious plans and is always looking for power, Naruto and Ino might have to deal with him all over again as they travel back in time. He could be trying to interfere with their attempts to change the past.
Danzo Shimura might be another one. He is very secretive and power - hungry. If Naruto and Naruko's time - traveling actions expose his dark deeds or interfere with his control over the village, he would become their enemy. He has many underhanded methods and a strong influence within the village that they would have to deal with.
Maybe some of the historical villains who were thought to be dead. If Naruto and Tenten's time travel disrupts the natural flow of time, it could bring back villains like Orochimaru in his prime or some ancient evil ninja clans that were long forgotten. They would see Naruto and Tenten as threats to their re - emerging power.
One possible main antagonist could be Madara Uchiha from an earlier time period. If Naruto and Kyshina travel back far enough, they might encounter a younger and more power - hungry Madara. He could be a major obstacle as he tries to achieve his early goals of creating a world under his control, which would be in direct opposition to what Naruto and Kyshina are trying to do to protect the future of the village.