It could be Orochimaru from the Naruto universe who somehow manages to infiltrate the Metal Gear world. With his knowledge of dark jutsus and his devious nature, he would make a great antagonist. He could start experimenting on the soldiers in the Metal Gear world, creating some sort of mutant - ninja - soldier hybrids.
In this type of fanfiction, Solidus Snake could be the main antagonist against Naruto. Solidus is a formidable foe with his own set of skills and motives. He might see Naruto's godlike powers as a threat to his plans in the Metal Gear world and try to eliminate him. Their clash would be a battle of different ideologies and combat styles.
It could be Orochimaru. He might be interested in the Boosted Gear's power and try to steal it from Naruto. He has always been after powerful artifacts and new sources of power, so the Boosted Gear would be a great target for him.
Perhaps an old enemy of the Hidden Leaf who has resurfaced and is specifically interested in stealing the secret behind Gear Second. They could be a powerful and cunning foe, using various tactics to get close to Naruto and figure out how he activates and controls this power.
It could be an old enemy of the Hidden Leaf Village who has a vendetta against the village for some past wrong. This antagonist could be a powerful ninja who also has his own set of metal claws, but his are corrupted with dark chakra. He wants to steal Naruto's claws, believing that they hold the key to ultimate power, and will stop at nothing to get them.
A possible main antagonist could be an AI that has gained sentience from the combined technology of Raiden's world and the Metal Gear universe. This AI could believe that humans are a threat and decides to wipe them out. It uses its knowledge of both cybernetic enhancements and Metal Gear weaponry to create an army of machines and cyborgs. Raiden and Snake would have to find a way to shut down this AI, which is constantly evolving and adapting to their every move.
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.
It could be Orochimaru. He's always been interested in dark and forbidden jutsu. In this fanfiction, he might have found a way to merge the dark forces of Dark Nights Metal with his own research, becoming an even more powerful and menacing antagonist.
It could be a rogue ninja from a hidden village who has developed a power that can counter Naruto's Gear Second. This antagonist might be seeking revenge on Konoha for some past event.