The Akatsuki remnants could still pose a threat. Members like Sasori or Deidara might have had backup plans or followers who now want revenge for the Akatsuki's downfall. They could target Naruto specifically, seeing him as the one who brought down Pain and disrupted their plans.
Maybe Orochimaru's former followers who are still lurking in the shadows. They see Naruto as a threat and Hinata as an easy target to get to Naruto. Another possibility could be some power - hungry shinobi from other villages who view Konoha as weak after the Pain incident. They might target Naruto and Hinata as key figures in Konoha's future to try and undermine the village's rebuilding efforts.
Danzo could be a main antagonist. He's always been power - hungry and has seen Naruto as a threat to his control over the village. After Pain's attack, he seizes the opportunity to turn the villagers against Naruto.
It could be a group of powerful mafia bosses who see Naruto's ninja abilities as a threat to their illegal operations. They might try to hunt him down and eliminate him before he can expose their secrets or interfere with their business.
It could be some rogue ninjas who were against the peace treaties after the war. They might form a group and try to disrupt the newly - established peace in the ninja world.
Some of Naruto's former friends who have been influenced by the negative propaganda against him could also be antagonists. They might be misled into believing that Naruto has changed for the worse. They could actively oppose Naruto, either by trying to capture him or by preventing him from doing certain things. Another possibility is that there could be a hidden group within the village that has a vendetta against Sasuke and, by extension, Naruto for bringing him back.
A new main antagonist could be a forgotten or banished god. There are many minor gods in Greek and Roman mythology that haven't been explored much. One of them could be angry at the demigods for getting all the attention and decide to cause chaos. For example, a god of misfortune who decides to curse the demigods with a series of bad luck that leads to dangerous situations.
In this 'naruto after pain invasion fanfiction', Naruto is central, of course. But characters like Jiraiya could be important even though he's dead. His teachings and memories could still influence Naruto's decisions. Iruka, Naruto's first teacher, might have a role in helping Naruto deal with his emotional state. Gaara, as Naruto's friend and the Kazekage, could come to Konoha to offer assistance and strengthen the bond between their two villages. And then there are the other members of Naruto's team, like Kiba and Shino, who could be involved in various tasks related to the post - Pain invasion situation in Konoha.
There could be a new group of villains who emerged from the shadows. They might have been observing the war and learned from the mistakes of previous antagonists. They could be more powerful and cunning, perhaps using new forms of jutsu or technology that were developed during the war. Maybe they are after some ancient artifacts or secrets that were unearthed during the Fourth Great Ninja War.
Maybe it could be a former ally of an old villain who has a vendetta against Spider - Man for defeating their boss. They could be seeking revenge and causing new crimes in the city.
One potential antagonist could be a group of rogue ninjas who see Sarada's pregnancy as a sign of weakness in the village. They might try to target her to cause chaos. Another could be a jealous rival who doesn't like the attention Sarada is getting due to her pregnancy and her connection to Naruto.