Maybe the main antagonist is a rogue scientist who has been experimenting with the combination of Raiden's body enhancements and Metal Gear technology. He wants to create a new type of super - being that he can control. He kidnaps innocent people to use as test subjects and is willing to sacrifice anything to achieve his goal. Raiden and Snake must stop him before he creates a monstrosity that could destroy both of their worlds.
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.