A new character could be introduced as the antagonist. Maybe someone who has also time - traveled and has their own agenda for the past. This character could be trying to preserve the original timeline for some reason, or they could be trying to create an even worse future. They would oppose Obito and Kakashi at every turn, creating a lot of conflict and drama in the fanfiction.
Danzo could be a great antagonist. If Kakashi travels back in time, Danzo's underhanded plans, like his control over Root and his desire for power, would still be in motion. He'd likely oppose Kakashi's attempts to change things for the better, especially if it threatened his own influence.
One common theme is redemption. Since they both have a lot of regrets in their original timeline, time travel gives them a chance to fix things, like saving their friends or preventing the destruction of the village.
It could be Madara. Even if Obito goes back in time, Madara's long - term plans for the ninja world are still in motion. He might be the main force that Obito has to oppose as Madara's ideas often lead to destruction and chaos.
One idea could be that Obito and Kakashi are sent back to their childhood days. Obito then tries to prevent certain tragedies that happened in their past, like the death of his comrades. He might also try to change Kakashi's cold - hearted nature that developed over time. This could lead to a whole new set of relationships and events in the Naruto world.
A new antagonist could be a time - traveling ninja from another dimension who doesn't want Obito to change the past. This ninja might have his own plans for the Naruto world and sees Obito's interference as a threat. Or perhaps it could be an old enemy of the Uchiha clan who was thought to be dead but resurfaces in this new timeline because of Obito's time - traveling. They could be more powerful than before and have a vendetta against the Uchiha and anyone who tries to change their fate.
One common theme is redemption. Since they go back in time, both Obito and Kakashi often try to atone for their past mistakes. For example, Obito might try to prevent the events that led him to become evil in the first place.
A plot could be that there is a prophecy about Female Kakashi and Obito saving the ninja world together. They initially don't believe it, but as events unfold, they are forced to work together. Through their journey, they develop a deep connection and eventually fall in love.
Cell could be a great antagonist. Imagine Goten travels back in time to before Cell was complete. Cell could sense Goten's power and try to absorb him to become even more powerful. This would put Goten in a tough situation where he has to avoid Cell while also trying not to disrupt the timeline too much.
It could be a time - traveling villain who is trying to disrupt the timeline for their own gain. This villain might be trying to erase certain events or people from history to change the future in a way that benefits them.
It could be a time - traveling sorcerer who wants to change history for his own evil purposes and sees Achilles as a threat. The sorcerer might try to stop Achilles from getting back to his own time or use his knowledge of the future to his advantage against Achilles.