A new character could be the main antagonist. For example, a rogue ninja who has mastered a unique and powerful jutsu that allows him to control the very fabric of the war game. He could be someone who was once shunned by the ninja world and now wants revenge. He sets up the war game with the intention of destroying the major ninja villages and creating his own order. He uses his knowledge of the ninja world and his special jutsu to create impossible - to - beat scenarios for the heroes in the war game.
Madara Uchiha could be a great antagonist in this kind of fanfiction. He has the power and the ambition. He could manipulate the war game from behind the scenes, perhaps using his Sharingan to control the minds of some of the participants. He wants to reshape the ninja world according to his own vision, and the war game provides him with an opportunity to do so without directly confronting all the ninja forces at once.
Perhaps a secret organization within the Hidden Leaf that wants to take over the village. They use Naruto as a scapegoat, getting him banished so they can carry out their evil plans without interference from Naruto. They would be the main antagonists as they are the ones behind the false accusations and the push for his banishment.
Perhaps a new, unknown force. With Naruto gone, a previously hidden group with a vendetta against the ninja villages could emerge. They might blame the villages for the destruction caused during the war and see Naruto's death as the perfect time to strike, when the villages are still recovering and vulnerable.
It could be a rogue ninja who took advantage of the chaos during the war. This ninja might have been gathering power in the shadows and now sees Naruto as a threat to his plans.
Maybe it's a rogue AI within the singularity game. This AI has become self - aware and believes that Naruto and his ninja powers are a threat to its existence. So it starts creating all kinds of obstacles and enemies within the game to stop Naruto from leaving or to defeat him. It might even try to corrupt Naruto's chakra system with digital viruses.
A group of former war criminals who were pardoned but now want to take over the ninja world. They might have formed a secret organization during their time in prison or exile. They could be using new, dark jutsus that they developed in secret to try and overthrow the current leadership in the villages and establish their own rule.
It could be Orochimaru. In this fanfic, he could be a player of the same 'life - game' as Naruto, but with a much more sinister goal. He might be trying to manipulate the game rules to his advantage, like finding a way to make all the ninja in Konoha his puppets. Naruto would then have to figure out how to stop Orochimaru's evil plans within the game - like mechanics of his world.
It could be some of the traditionalist elders in the Hidden Leaf. They might see Naruto as a threat even after the war, fearing his growing power and influence, and thus engineer his banishment. So they could act as antagonists as Naruto tries to find his place outside the village.
Madara Uchiha might also be a main antagonist. His goals of reshaping the ninja world could be directly opposed to what Naruto is trying to achieve with his newfound 'godlike' powers. Madara would likely see Naruto as a major obstacle in his grand plan for the shinobi world.
It could be a long - lost relative of Orochimaru. This person might have been secretly studying Orochimaru's forbidden jutsu and developed even more terrifying techniques. They could be seeking revenge on the ninja world for ostracizing Orochimaru.
It could be someone from the Naruto universe who doesn't like Naruto's newfound fascination with Aku. For example, Danzo might see Naruto's interest in Aku as a threat to the stability of the village and try to stop Naruto from further exploring Aku - related things. So, Danzo could be the main antagonist in this case.