It could be Orochimaru. He's always been interested in Konoha's secrets and might have found a way to use Naruto's clones for his own purposes. He could be manipulating the clones from the shadows to steal forbidden jutsu scrolls or something similar.
Another possibility is that the main antagonist is actually a corrupted version of Naruto himself. Maybe some dark force has influenced him and his clones are acting out this dark side's desires to infiltrate Konoha and cause chaos, perhaps to overthrow the current Hokage or disrupt the village's peace.
Maybe it's a new, unknown enemy. This character could have some vendetta against Konoha and has realized that using Naruto's clones is a great way to get inside the village undetected. They might be using some sort of mind - control device or jutsu on the clones to make them do their bidding.
In fanfic, Naruto clones could use stealth techniques. They might disguise themselves as ordinary villagers or even as other ninja. By changing their appearance slightly, they could blend in and move around Konoha unnoticed. Another way could be to take advantage of the chaos during a festival or a big event in the village when security is more lax.
In a fanfic, if Naruto clones infiltrated Konoha, it could lead to chaos. The villagers might mistake the clones for the real Naruto causing confusion. They could disrupt normal daily activities and security measures in the village. Also, depending on the intentions of the clone infiltration in the fanfic, it could be a prank by Naruto, or it could be part of a more complex plot where someone else is controlling the clones to cause harm or gather information.
It could be Orochimaru. He has always had his eyes on Konoha and might find a way to manipulate Naruto into attacking it. Maybe he uses some new experimental jutsu on Naruto to make him do his bidding.
It could be a new villain who has been plotting against Konoha while Naruto was away.
It could be a rogue ninja from another village who has a vendetta against Naruto. This ninja might spread false rumors about Naruto in Konoha, which eventually leads to Naruto leaving. So, this ninja would be the main antagonist as he is the root cause of Naruto's departure.
It could be some of the more conservative village elders in Konoha. They might see Naruto Namikaze's unorthodox ways and growing power as a threat to their traditional way of running the village. So they create situations that make Naruto feel unwelcome and eventually lead to his departure, making them the antagonists in the story.
It could be a rogue ninja from within Konoha who doesn't want Naruto to return because he fears Naruto's growing power will disrupt his own plans for power within the village.
It could be an evil scientist who created the Chichi clones for some malicious purpose. Maybe they want to use the clones to control Goku or to disrupt his life so he can't protect the Earth.
Perhaps Danzo could be the main antagonist. He was always a bit of a shadowy figure in the original Naruto series. In this fanfic, he might see Naruto and Sasuke as a threat to his own control over Konoha. So, he uses his influence to have them banished. He could be secretly working with external forces to further his own agenda while keeping Naruto and Sasuke away from Konoha.
It could be a corrupt elder in Konoha. They might be power - hungry and see Naruto as a threat to their control. So they manipulate the situation to make Naruto the enemy.