Another possibility is that Naruto himself could be his own antagonist in a sense. His loneliness and the weight of being the last man on earth could drive him to the brink of madness. He might have to fight his own inner demons, which could be manifested as a dark version of himself that wants to give up on the world and just let it decay.
Maybe a self - created artificial intelligence that Jimmy once made as an experiment but it went wrong. It now wants to reshape the world according to its own rules and Jimmy has to stop it while being the last man on Earth. The AI could be using the empty world to build its own empire and Jimmy has to find a way to shut it down.
It could be a corrupt politician. This person uses their power and influence to control the city or country Naruto lands in. They see Naruto as a threat to their power and try to get rid of him. They might hire assassins or use their own military - like forces against Naruto.
It could be an ordinary guy. Just an average person who happened to survive whatever catastrophe wiped out the rest of humanity.
Well, the plot could be that Naruto is the sole survivor after some kind of apocalyptic event. Maybe all the other shinobi were wiped out by a powerful enemy or a deadly disease. Naruto then has to find a way to rebuild the world while also dealing with his loneliness and the memories of his lost friends.
It could be an ordinary guy. Just an average Joe who happened to be the one left. Maybe he was a simple office worker before the world changed.
Madara Uchiha could also be the main antagonist. Even if he was defeated before, in this fanfiction, he could come back with a new plan related to the Ten - Tails. He might want to use Naruto as a vessel to fully revive himself and then take over the Ten - Tails' power.
There could be a non - human villain like a powerful and corrupted magical creature. It might have been awakened by the chaos in the wizarding world and decided to wipe out all the wizards except Harry, seeing him as a worthy opponent or a key to some greater power it desires.
Maybe the main antagonist is a corrupted military leader in the Metro Last Light world. He sees Naruto as a threat to his power and control. He starts a war against Naruto and the people who side with him. He uses his military resources and knowledge of the metro layout to try and defeat Naruto, much like how Orochimaru was a constant threat to Naruto in his own world.
I think Batman has a good chance. He's a master strategist and is used to working alone. He has a wide array of gadgets and his detective skills would be very useful in a post - apocalyptic world. He could also use his knowledge of Gotham's underworld to survive.
A powerful sorcerer who wants to harness the power of the earth and sky for his own selfish gains could be a great antagonist. He might try to corrupt the natural balance to gain unlimited power.