It could be a senior officer who has a grudge against Percy for some reason. Maybe Percy accidentally made him look bad in front of the higher - ups early on.
In some cases, the antagonist could be an external force. For example, a group of pirates that the navy is trying to combat, and one of their leaders specifically targets Percy because he sees him as a threat to their operations.
There might be a fellow sailor who is jealous of Percy. If Percy shows great potential or gets special attention, this jealous character could try to undermine him at every turn.
It could be a powerful sorcerer who wants to steal Percy's powers. Since Percy might have some unique abilities, this sorcerer sees her as a key to gaining more power for himself. He could be creating chaos in the city to draw Percy out and then try to defeat the Avengers when they come to her aid.
There's a chance that it's a new entity created by the imbalance between order and chaos. This entity is a force of pure destruction and wants to tip the scales completely in favor of chaos. Percy, Nico and Jason, with the help of Chaos, have to stop this entity from achieving its goal.
There might be a supernatural or magical antagonist, even in a military setting. This could be a dark wizard or a creature that has infiltrated the military for its own malicious purposes. Harry, with his experience in the magical world, would be the key to dealing with this threat, but he has to convince the non - magical military personnel of the danger first.
It could be one of the traditional Volturi members who oppose Edward's presence. They might see him as an outsider who could disrupt their long - established order. For example, Caius might be against Edward joining as he's often portrayed as more rigid and less accepting of new vampires in the Volturi.
Perhaps an old enemy of one of the members of Team 9 shows up. Since Naruto has joined the team, they might see it as an opportunity to get revenge. This antagonist could be someone who was once defeated by the member's family and now wants to prove themselves. They would be very cunning and use their knowledge of the team member's past to try and divide the team.
It could be Voldemort. Imagine if he somehow found a way to cross over into the world of the Fellowship. He would be a powerful and menacing antagonist, using his dark magic to oppose both Harry and the Fellowship.
It could be Voldemort. Even if it's a fanfiction where Harry joins Tom, Voldemort's future self might still be a threat and oppose Harry's attempts to change Tom.
It might be an alien race that has the ability to travel through the earth's crust undetected. They are stealing valuable resources from the planet's core. The Avengers, including Quake, are the only ones who can stop them. The aliens' technology and physical abilities make them a formidable foe, and Quake has to use her powers in creative ways to expose and fight them.
It could be an old enemy who has resurfaced, like Orochimaru again. Since Naruto and Sasuke are together now, Orochimaru might see them as a threat to his own plans for power and immortality.
There could be her drill sergeant, a tough but fair person who helps shape Bella into a proper navy personnel.