It could be the remaining Otsutsuki clan members. Since Naruto has merged with Kaguya, they might see this as a threat to their plans for the ninja world or a perversion of their bloodline. They could try to either eliminate the merged Naruto - Kaguya or control it for their own purposes.
Perhaps some of the more power - hungry ninja leaders who fear the new power that Naruto - Kaguya represents. They might think that this new entity will disrupt the power balance they've established. So, they could form an alliance against the merged being, making them the antagonists in the story.
There could be ancient evils that were sealed away long ago and are now awakened by the powerful chakra signature of the merged Naruto - Kaguya. These evils, having been dormant for so long, see this new power as a way to break free completely and cause havoc, thus becoming the main antagonists as they oppose the merged entity's attempts to maintain peace in the ninja world.
There could be a group of rogue shinobi who fear Kaguya's power and Naruto's influence on her. They might believe that having Kaguya in the world again, even if she is being 'raised' by Naruto, is a threat to their own plans for power and domination. So they try to stop Naruto and eliminate Kaguya.
One potential antagonist could be those who fear Naruto's new - found godlike powers. There might be ninja from other villages who see Naruto as a threat to the balance of power. Another could be remnants of Kaguya's old enemies who resurface, seeing Naruto as a continuation of Kaguya's influence and wanting to stop him. Also, there could be dark forces within the ninja world that want to corrupt Naruto's new powers for their own evil purposes.
One interesting plot could be the exploration of new powers that emerge when Naruto and Kaguya are merged. For example, perhaps a new form of chakra that combines Naruto's life - affirming energy with Kaguya's ancient and powerful chakra. Another plot might involve how the ninja world reacts to this new entity. Do they see it as a threat or a new source of hope? Also, the merged Naruto - Kaguya could have a unique perspective on the history and future of the ninja world, which could lead to revelations about hidden secrets or new ways to prevent future disasters.
The Otsutsuki clan members other than Kaguya could be antagonists. Since Kaguya is training Naruto, they might see Naruto as a threat to their plans.
There could also be some original characters created specifically for this fanfiction. For example, a powerful ninja who has knowledge about the merge process and tries to either help or hinder Naruto. Or perhaps an ancient spirit that was somehow involved in the creation of Dark Naruto in the first place and now has an interest in the merge.
Sasuke would most likely be involved. Since he has a strong bond with Naruto, he would sense something is wrong and try to free Naruto from Kaguya's control. Sakura might also be part of it as she cares about Naruto and would be determined to save him. Kakashi could play a role too, using his wisdom and experience to figure out a way to break Kaguya's hold on Naruto.
Well, the main antagonists could be a group of rogue ninja who are hired by a powerful nation to take down Naruto. Since he is unkillable, they would have to use more underhanded tactics like trying to isolate him from his friends and allies. Or perhaps there is a dark force that is awakened by Naruto's unkillable state, thinking that he is a threat to the balance of the ninja world. This dark force could then become the main antagonist, trying to destroy Naruto at all costs.
Obviously Naruto would be one of the main characters since it's about him being the heir of Kaguya. Sasuke could also be a main character as Naruto's rival and friend. Sakura might be involved too, as she is part of Naruto's team. And there could be other characters like Kakashi, who would play a role in guiding Naruto as he discovers his new identity. There might also be some new characters introduced that are related to Kaguya's past, who either help or hinder Naruto on his journey.
Sasuke can also be involved in some cases. Since he and Naruto are often together in many situations, Sasuke's presence might add some complexity to the relationship between Kaguya and Naruto. For example, Sasuke might be suspicious of Kaguya's intentions towards Naruto at first.
It could be a rogue ninja who wants to use the descendant for their own power - gain. Maybe someone who believes that by controlling the descendant, they can access Kaguya's ultimate power. For example, a power - hungry ninja who has been researching Kaguya's secrets for a long time.