There could be new antagonists created specifically for this fanfic. Maybe a group of time - traveling ninjas who don't want Naruto to change the past because it would disrupt their own plans. They could have their own motives and powers that Naruto has to face.
Another possibility is that the Akatsuki members, who were major antagonists in the original series, could be involved in a different way in this fanfic. Maybe they are working with someone from the past who has a vendetta against Naruto's family, and Naruto has to figure out their connection and stop them to rescue his family.
It could be the same antagonists from the original Naruto series who were involved in the events that led to his family's misfortune. For example, Orochimaru might be one of the main antagonists as he was always after power and could have been involved in something related to Naruto's family.
It could be Orochimaru. He has always been interested in power and the secrets of the tailed beasts. So, he might see Naruto and the Jinchuuriki family as a source of great power to experiment on or steal from.
One interesting plot point could be Naruto using his knowledge from the future to outwit his enemies more easily in the past while on the mission to rescue his family. For example, he might know the weaknesses of certain villains he didn't before.
It could be some hidden members of Naruto's family itself. Maybe there are relatives who have been manipulating things from the shadows and their actions led Naruto to believe he needs to take revenge on the family as a whole.
The elders of his family or clan could be the main antagonists. They might have exiled Naruto in the first place due to some old - fashioned beliefs or fear of his power. Throughout the fanfiction, they could try to stop Naruto from finding out the truth or coming back to the clan.
His family members themselves could potentially be antagonists in a sense. If Naruto is rejecting them, there could be some family members who try to stop him from leaving or try to change his mind forcefully. They might see his rejection as a threat to the family's reputation or unity.
Another common antagonist could be a powerful and mysterious dark wizard - like figure who has an interest in Hinata's unique abilities. This figure might be from a far - off land and has come to the Naruto universe specifically to capture Hinata. Naruto has to face this unknown and powerful foe to save her, which usually involves a lot of adventure and discovery as he tries to understand the enemy's powers.
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 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.