Well, it could be Orochimaru. Even if they travel in time, Orochimaru's thirst for power and knowledge might make him an antagonist. He could see Sasuke and Shikamaru as threats to his plans, especially if they are trying to change the past which might interfere with his own schemes.
Madara Uchiha might also be a main antagonist. If they travel to certain points in time, Madara's grand plans for the ninja world could put him at odds with Sasuke and Shikamaru. He is powerful and has his own vision, which might not align with what Sasuke and Shikamaru are trying to achieve in their time - traveling adventure.
In some 'naruto shikamaru and sasuke time travel fanfiction', Danzo could be an antagonist. His shadowy and often self - serving actions in the original Naruto story make him a likely candidate. If Sasuke and Shikamaru's time travel actions threaten his power or his hidden agendas, he would surely oppose 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.
Madara Uchiha could be an antagonist as well. Even if they travel back to a time before his grand plans were fully in motion, he would still be a very powerful and dangerous foe. He might sense that Naruto and Shikamaru are from the future and try to use their knowledge for his own purposes, or simply eliminate them if they stand in his way.
One great Naruto, Sasuke, and Shikamaru time travel fanfiction is 'A New Beginning'. It has an interesting plot where they travel back to change key events in the ninja world. The character development is on point, and it really delves into how their knowledge of the future affects their actions in the past.
Another possibility is a new and powerful enemy from a neighboring village. This enemy might view fem Naruto as a symbol of the strength of her village and wants to take her out to weaken the village. Shikamaru then has to protect her from this external threat.
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.
There could be an outside force, like a neighboring village that wants to keep Naruto and Sasuke away from their own village. They might be afraid of the potential power and influence Naruto and Sasuke could bring back if they return. So, this neighboring village sends their best ninjas to hunt down Naruto and Sasuke during their banishment, making them the main antagonists in the fanfiction.
One interesting plot could be that they travel back to the time when the Uchiha clan was about to be massacred. Sasuke might try to change the fate of his clan, while Shikamaru uses his intelligence to strategize and deal with the political implications. They could face many challenges, like not being believed by the people of that time or accidentally causing more chaos.
Often, Orochimaru can be a main antagonist. Since he has his own devious plans in the Naruto universe, in a time - travel scenario, he might oppose Naruto and Tsunade's attempts to change things for the better. He could be trying to use the time - travel chaos to his own advantage, like stealing forbidden jutsu from different eras.