Perhaps an AI that has gone rogue within the game world. The AI sees the godlike gamer as a threat to its own existence or its plans for the game world. It could constantly create obstacles and send out powerful in - game creatures to attack the gamer.
It could be a rogue fallen angel who is jealous of the godlike SI's power. This fallen angel might see the SI as a threat to their own plans of ruling the underworld or causing chaos between the three factions in the High School DxD world.
It could be a powerful gamer from another dimension who wants to take over the Kenichi world. He sees it as just another level in his never - ending game of conquest and has no regard for the lives and values of the people there.
It could be an original character created specifically for the fanfiction. Maybe another gamer - like figure who has opposing goals to the Godlike Gamer OC. They might compete for resources or power within the Fate universe.
Another possibility is a powerful spirit from the Avatar world that has been corrupted by the introduction of Naruto - like powers. This spirit could resent the intrusion of this new power source and seek to destroy anyone associated with it. It might have unique abilities that combine the spiritual magic of the Avatar world with the raw power of Naruto's chakra, making it a formidable foe.
There's also the possibility that a group of rogue ninjas, who have banded together after being ostracized for their interest in the godlike hollow powers, become the antagonists. They might believe that Naruto is misusing or hoarding these powers and decide to take them by force, leading to a series of intense battles between them and Naruto.
Perhaps a dark entity from another dimension. This entity senses Naruto's powerful bloodline and wants to possess him or use his body as a vessel to enter the Naruto's world and wreak havoc. It would have otherworldly powers that Naruto has never faced before, making it a truly formidable antagonist.
It could be a combination of Orochimaru and Lex Luthor. Orochimaru from the Naruto universe is always seeking power and Lex Luthor from the DC universe is a brilliant but evil mastermind. They could team up, with Orochimaru being interested in Superman - like Naruto's unique physiology and Lex Luthor wanting to use Naruto's power to take over both the Naruto world and the DC world. They would be a formidable duo, constantly devising plans to undermine Naruto and his friends.
Perhaps a corrupt hospital administrator who wants to shut down House's unorthodox gaming - related medical experiments. This person sees House's methods as a waste of resources and a threat to the hospital's reputation. They would do everything in their power to stop House from continuing, creating a lot of conflict.
Maybe it could be a demigod who has become obsessed with power through gaming. This demigod, let's say a child of Hades, discovers a way to use dark magic and combine it with gaming technology to try and rule over all the other demigods. He sees Percy as a major threat to his plans because Percy is so popular and has strong powers, so he constantly tries to undermine Percy at every turn.
A tech - genius named Techno - Tyrant. He could be a former game developer who turned evil after his creations were rejected. He uses his knowledge of gaming mechanics and virtual reality to create dangerous traps for the Justice League.