Danzo could also be a common antagonist. He was very power - hungry and had his own dark secrets. In a time - travel scenario, he might view Kakashi and Naruto as threats to his control over the Hidden Leaf Village in the past. He could try to eliminate them to maintain his grip on power.
Madara Uchiha is another one. He had grand plans for the future of the ninja world. If Naruto and Kakashi travel back in time, Madara might see them as obstacles to his long - term plans. He might try to use his Sharingan and his knowledge of the past to outwit them and continue on his path of destruction.
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.
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.
Naruto is often a common character. Since Naruto has a strong bond with Kakashi, he might be involved in Kakashi's time - traveling adventures. Sasuke could also be there. Their relationship with Kakashi in the original story makes it likely for them to show up. And of course, Guy would be a great addition. His friendly rivalry with Kakashi would add some humor and action to the time - travel scenarios.
The village elders could be antagonists. They might see Naruto and Kakashi as threats to their traditional way of ruling the village and use false accusations to banish them.
Danzo might be an antagonist. He's always been power - hungry and might see Naruto as a threat, especially if Kakashi is guiding and protecting him. Danzo could try to undermine Kakashi's efforts to raise Naruto and might even send his root agents to spy on them or cause trouble.
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.
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.
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.