Perhaps an old enemy from Naruto's past that was thought to be defeated has resurfaced. This enemy might have targeted Naruto's wife as a way to get revenge on Naruto for their previous defeats. They could be using her as a bait to lure Naruto into a trap.
It could be a rogue ninja who has a vendetta against Naruto. This ninja might see Naruto's son as a way to get back at Naruto for past defeats or slights.
A possible main antagonist in such a fanfic could be a dark entity that has possessed someone close to Naruto. This entity could be using the host's body to get close to Naruto and then attacks him, resulting in the loss of his arm. Naruto would then have to figure out not only how to deal with his injury but also how to save his friend from the dark entity's control.
It could be a rogue ninja from another village who has a long - standing grudge against Naruto. Maybe this ninja has been plotting for years to take revenge on Naruto and when Naruto fakes his death, he starts to target Naruto's friends and family instead, thinking it will draw Naruto out.
It could be a new character, a rogue ninja from a long - lost clan. This antagonist might have a vendetta against Naruto because they see his potential to awaken the Rinnegan as a threat to their own plans for power. They could be trying to stop Naruto from achieving this new level of power so that they can carry out their evil deeds unopposed.
It could be Orochimaru. He's always been interested in Naruto's power. Maybe he devises a plan to make Naruto lose his memory so he can manipulate him more easily, perhaps to use him as a weapon against the Hidden Leaf.
Another possibility is that the main antagonist is a group. It could be a secret organization that Naruto discovers is plotting something big. Since they are so powerful and well - connected, Naruto fakes his death to infiltrate them and expose their plans from the inside.
It could be a relative from his family who was behind the abandonment. Maybe they want to keep Naruto away from some family secret or power, and they will do anything to stop him from finding out the truth.
Maybe it's an evil organization that wants to isolate Naruto. By making his family forget him, they hope to break Naruto's spirit and prevent him from becoming a powerful force in the ninja world. So they target his family's memories as a way to get to him.
It could be Kaguya. If Kaguya were to return and use her powerful abilities to drive Naruto mad, perhaps by invading his mind with dark thoughts and memories. She has the power to warp reality and minds, so she could easily make Naruto lose his sanity. And since she has a grudge against the world of ninjas, making Naruto, one of the most powerful ninjas, go insane would be a great way for her to start her reign of terror all over again.
A new and mysterious dark ninja could be the main antagonist. This character might have a special ability to corrupt others. They target Naruto specifically because of his power and influence. By using some form of dark jutsu or psychological manipulation, they make Naruto lose his humanity, turning him into a weapon against the very people he used to protect.