In this fanfiction, it's possible that an ancient and powerful beast is the antagonist. The beast might have captured Pyraa to lure Naruto into a trap. Naruto will need to use all of his skills, including his Sage Mode if necessary, to defeat this beast and save Pyraa.
Well, perhaps Naruto could use his shadow clone jutsu to create multiple copies of himself to distract the enemy while he rescues Pyraa. He might also use his Rasengan to break through any barriers in the way.
One possible antagonist could be the Akatsuki members. They are always looking for strong opponents or valuable information. Maybe they target Iruka because they think he has some knowledge about Naruto that they can use, and Kakashi has to stop them.
One possible antagonist could be Orochimaru. He has always been interested in Naruto for his Nine - Tails power, so it would make sense for him to be a threat that Kakashi has to protect Naruto from.
One possible antagonist could be Orochimaru. He might be interested in Kim's unique skills and gadgets for his own evil experiments. He could set a trap for her and Naruto would have to save her from Orochimaru's clutches. Another could be Drakken. He might team up with some ninja villains, like the Akatsuki members, in order to achieve his own goals. Naruto and Kim would then have to face this combined force.
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.
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 potential antagonist could be a power - hungry shinobi from another village. They might view Hayate as a threat to their plans, maybe because Hayate is involved in some sort of peace - keeping mission between villages. So, they try to eliminate him. And Naruto, being the defender of his comrades, will not stand by and let that happen. There could also be a group of missing - ninjas who band together to take on Hayate, thinking he's an easy prey, but they underestimate Naruto's loyalty and strength.
It could be some dark magic users from Lucy's world who see her as a threat. They might be trying to stop her from using her magic for good.
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.
In this fanfiction, it's possible that a symbiote - influenced villain could be the antagonist. Maybe someone who has bonded with a part of the symbiote and has a thirst for chaos. They might see Flash as an easy target to cause mayhem and draw out Spider - Man. Additionally, the Scorpion could be another antagonist. He might be hired by some shadowy figure to capture Flash in order to lure Spider - Man into a trap. There could also be a group of alien invaders who mistake Flash for someone important and Peter has to save him from their clutches.