It could be a rogue ninja who has mastered side sleep and uses it for evil purposes. This ninja might be seeking power and domination over the ninja world and sees Naruto as a threat to his plans. He uses side sleep to manipulate others and create chaos, and Naruto has to stop him.
There could be a group of ninjas who have formed a cult around side sleep. They believe that side sleep is the key to ultimate power and are willing to do anything to protect their secrets. Naruto stumbles upon their activities and becomes their target. The leader of the cult, a powerful and fanatical ninja, then becomes the main antagonist as Naruto tries to expose and stop their dangerous practices.
Perhaps an ancient spirit that is somehow related to side sleep. This spirit has been awakened after a long slumber and is causing havoc in the ninja world. It can possess people when they are in side sleep and make them do its bidding. Naruto, being the hero, has to find a way to exorcise the spirit and put an end to its reign of terror.
The fanfic could be about Naruto's training against side sleep. Naruto realizes that side sleep is a state that can enhance a ninja's chakra control if mastered properly. However, it's extremely difficult to enter this state consciously. So, he starts training with Kakashi and Sakura. Kakashi tries to teach him some mental techniques while Sakura helps him with the physical aspects of relaxation. After many failed attempts, Naruto finally manages to enter the side sleep state and finds that his chakra has become much more powerful and refined.
One possible plot could be that Naruto and Shikamaru are on opposing sides in a strategic battle. Naruto might be brash and ready to go all - out, while Shikamaru is using his intelligence to outwit Naruto. Maybe it's a sparring match within the Hidden Leaf village where they have different goals. Naruto could be aiming to prove his strength, and Shikamaru is trying to show that brains can overpower brawn. They might start with some basic jutsu exchanges, and as the fight progresses, Naruto realizes he needs to use more than just his raw power to defeat Shikamaru.
It could be a long - lost moon - dwelling ninja clan that has a grudge against the Leaf Village. They see Naruto as a threat to their plans on the moon's dark side.
The Hidden Leaf Village elders could be the antagonists. If Naruto has gone against their rules and become an S - rank criminal, they would send out their best ninja to stop him. They might view Naruto as a danger to the stability of the village, even if his actions were for a good cause. This could create a very complex dynamic, as Naruto has to fight against the people he once called family.
The Organization in the Claymore world could be the main antagonist. They already have a lot of secrets and do some morally ambiguous things. If Naruto shows up and starts changing the status quo, like teaching Claymore warriors to be more independent, the Organization might see him as a threat and try to eliminate him.
It could be a rogue ninja who was once a student of Orochimaru and has now developed his own dangerous jutsu. He wants to take over the ninja world and believes the old ways are holding everyone back.
Orochimaru could be a great antagonist. He might want to use Shenron's power for his own dark experiments. He could try to steal the dragon balls and manipulate the wishes to gain immortality or create an army of powerful, immortal ninja.
It could be someone who opposes Naruto's newfound admiration for Ganondorf. Maybe a traditionalist ninja who thinks Naruto is straying from the true ninja path by getting influenced by Ganondorf.
Lex Luthor could be a great antagonist. He's always looking for power and knowledge. If he discovers Naruto's abilities, he might try to use them for his own gain or see Naruto as a threat to his plans in Smallville.
It could be Orochimaru. He's always been interested in unique powers and abilities. The idea of X - 23's mutant abilities and Naruto's jinchuriki powers would be very appealing to him. He might try to capture them both to use in his experiments to gain ultimate power.