The other shinobi villages might also be antagonists. If Naruto's village is seen as a threat because of his power, they could target him. This would make Naruto angry as he's being attacked for no good reason other than fear. Their actions against him and his village could lead him to a darker state as he has to fight back against these external threats.
Sasuke could also be an antagonist in some dark angry Naruto fanfiction. If Sasuke's path of revenge takes a turn where he becomes a true enemy of Naruto, not just a rival, it would really push Naruto into a dark and angry place. Their conflict could be much more intense than in the original story, with Sasuke representing everything that is wrong with the shinobi world in Naruto's eyes at that moment.
Another likely antagonist could be the government or some secret agency. They might see Danny as a threat because of his powers. In an angry fanfiction, they could be constantly trying to capture or study him, which would fuel Danny's anger. And Danny would have to fight against them to protect himself and his loved ones.
It could be an evil version of Sasuke. In the original story, Sasuke had his dark moments, and in a very dark fanfic, he could be fully consumed by evil and oppose Naruto in a much more malevolent way.
Perhaps some rogue ninja from other villages. They might see Naruto as a symbol of Konoha's power and want to take him down to weaken Konoha. These rogue ninjas could be led by a powerful and vengeful shinobi who has a grudge against Konoha. So when Naruto is alone on a mission or something, they attack, and that's when Minato steps in to save him.
Maybe some new rogue ninja group that has a vendetta against the Uzumaki family. They see Boruto as a way to strike at Naruto, so they try to harm him, which then leads to Naruto having to save him.
There could be internal antagonists within Naruto's own village. Some of the more conservative ninja in the village might not trust Naruto's new - found skills and powers obtained from Zetsu. They could try to undermine Naruto or even attempt to exile him, fearing that he has been corrupted by Zetsu's teachings.
The Akatsuki could still be the main antagonists. Since Naruto is being trained by Shisui, they would see Naruto as an even greater threat. His new skills under Shisui's training could put their plans at risk. For example, if Naruto becomes better at stealth and infiltration, he could disrupt their operations more effectively.
It could be some rogue ninja clans that are after Karin for her special abilities. They might see her as a tool to gain power or information. For instance, a clan that specializes in blood - related jutsu might want to use Karin's unique blood - sensing ability for their own evil purposes.
One possible antagonist could be a rogue ninja from another village. They might target Tenten for her unique weapon - handling skills, thinking they can use her to create powerful weapons for themselves. Naruto would then have to face this ninja to save Tenten.
The village elders could be antagonists. They might see Naruto and Kakashi as threats to their traditional way of ruling the village and use false accusations to banish them.