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.
Cell - like characters are often antagonists. Since Cell was such a major foe in the original series, new versions of Cell - like beings could be created in fanfiction to make Gohan angry. They might target his loved ones or the Earth itself, provoking Gohan's rage.
Sasuke could potentially be an antagonist. Even though they were friends before, Sasuke might see Naruto's new fused power as a threat to his own goals or ideals. He could challenge Naruto, thinking that Naruto's power is getting out of hand. Another could be some remnants of the Akatsuki. They might be interested in Naruto's new power and try to either steal it or use it for their own evil purposes.
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.
Madara Uchiha could be an antagonist as well. Even if they travel back to a time before his grand plans were fully in motion, he would still be a very powerful and dangerous foe. He might sense that Naruto and Shikamaru are from the future and try to use their knowledge for his own purposes, or simply eliminate them if they stand in his way.
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.
Well, it could be Orochimaru. He was always up to no good and had an interest in powerful ninja. He might target Naruto and Temari to either steal their powers or use them for his evil experiments, which would surely lead to them getting hurt.
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.
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.
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.
The Hidden Leaf Village itself could be an antagonist. If Naruto goes evil, the village that once was his home would be against him now.