The main antagonist could be a mysterious figure. This person could be targeting Clint for some unknown reason. They could be lurking in the shadows and when Clint least expects it, they strike and kick him in the balls. Throughout the fanfic, Clint could be on a quest to find out who this person is and why they did such a thing, which would drive the story forward.
Well, perhaps in this fanfic, Clint is involved in a sports event. He's a bit overconfident and an opponent accidentally kicks him in the balls. This could lead to a series of events where he has to face his own pride. His teammates might have different reactions, some feeling sorry for him while others might tease him a bit, which would all contribute to the story's development.
The villagers themselves could be the antagonists in a sense. They have always been somewhat afraid and resentful of Naruto because of the Nine - Tails. Their constant negative attitude towards Naruto could influence the decision to kick him out of Team 7. They might pressure the village elders and Kakashi into believing that Naruto is not a suitable member for the team and that he poses a threat to the safety of the other team members.
Perhaps a group of anti - technology extremists could be the main antagonists in an Ultron fanfic. They see Ultron as the symbol of all that is wrong with technology and are determined to take him down, no matter the cost. They might use their own advanced, but more rudimentary, technology to fight against Ultron. This would create an interesting contrast between Ultron's high - tech abilities and their more basic, yet effective, methods.
A rival medicine cat from another Clan might be the main antagonist. They could see Alderheart as a threat to their own status or the well - being of their Clan. So they might use dark magic or some underhanded tactics to bring about his death.
Vilgax could be a great antagonist. He could hack into the gaming systems to try and defeat Ben in a virtual world where the rules are different. He might use his advanced technology to create digital versions of his minions to attack Ben.
The Organization in the Claymore world could be the main antagonist. They already have a lot of secrets and do some morally ambiguous things. If Naruto shows up and starts changing the status quo, like teaching Claymore warriors to be more independent, the Organization might see him as a threat and try to eliminate him.
It could be a new alien species that Ben has never encountered before. This species could be territorial and see Ben as a threat to their planet where he's stranded. They constantly try to drive him away or capture him, which makes it difficult for Ben to find a way to leave.
It could be a rogue ninja who was once a student of Orochimaru and has now developed his own dangerous jutsu. He wants to take over the ninja world and believes the old ways are holding everyone back.
Orochimaru could be a great antagonist. He might want to use Shenron's power for his own dark experiments. He could try to steal the dragon balls and manipulate the wishes to gain immortality or create an army of powerful, immortal ninja.
One option could be an alien scientist who is obsessed with the power of the Nemetrix. He wants to study it and use it to create his own super - weapons. He might be from a race that has been at odds with the creators of the Nemetrix for centuries.