The restless souls on the ship itself could turn against Harry. Maybe they are so used to their cursed state that they don't want to be redeemed or set free, and they see Harry's attempts as a disruption to their eternal existence.
One possible plot is that Harry discovers that there is a greater purpose for him captaining the Flying Dutchman. He could be on a quest to redeem the souls on the ship by facing off against powerful dark forces that are linked to the curse of the ship. Along the way, he might make unexpected alliances with other magical beings from the sea world.
Since Harry is captaining the Aquila, he is a main character for sure. There might also be some of his friends or comrades who join him on this adventure. It could be that there are some original characters created by the fanfic author as well, who play important roles in the story, like a wise old mentor figure who gives Harry advice about captaining the Aquila, or a mischievous sidekick who gets into trouble and Harry has to bail them out.
A group of jealous students could be the main antagonists. They might be envious of Harry's natural talent and the attention he gets from the teachers. So, they try to sabotage his progress at the gifted school by setting him up to get in trouble or stealing his study materials.
Maybe a group of anti - magic fanatics within SHIELD itself. They see Harry's magic as a threat and try to undermine him at every turn. They could be secretly working with external forces that also oppose the use of magic in the world of SHIELD. Harry would have to prove that his magic can be an asset rather than a liability.
It could be a group of dark wizards who don't want Harry to succeed in becoming a cursebreaker. They might be using dark curses themselves to cause chaos in the wizarding world, and they see Harry as a threat to their plans. So they try to stop him at every turn, whether it's by setting traps or sending out cursed creatures after him.
Maybe there are some ancient dark wizards that Iskandr has a history with. These wizards could see Harry as a threat because of his potential, especially with Iskandr's training. They might emerge from hiding to try and stop Harry from reaching his full power, fearing that he and Iskandr together could disrupt their long - planned evil schemes.
There could be a group of dark wizards who are secretly operating within the Ministry itself. They oppose Harry's alliance with the Ministry because they fear that Harry will expose their illegal and immoral activities, like illegal potion - making or dark - magic experiments.
There could also be a new group of supernatural beings, perhaps a cult that worships dark magic. They might target Hellsing because of their power and the fact that Harry, with his wizarding abilities, is now part of the organization. This cult could be trying to summon some ancient and extremely dangerous entity, and Hellsing, with Harry's help, has to stop them.
There could be a secret society within the wizarding world that has long opposed the Knight Templars. They see Harry's new - found connection to them as a revival of an old threat. They try to undermine Harry and his attempts to bring the Templar values into the wizarding world by spreading false rumors and creating obstacles for him at every turn.
Some pure - blood wizarding families who value strict traditions and order might oppose Harry. They might view his very existence as an affront to their way of life. They could try to use their influence to drive him out of the wizarding community or plot against him in secret.