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.
The main character in the Flying Dutchman original story is the Dutch ship captain.
The main character is the captain of the Flying Dutchman. He is the one who is cursed along with his ship.
In Naruto Flying Dutchman fanfiction, Naruto is a must - have main character. His unique personality and abilities make him the focal point. The Flying Dutchman's captain is another main character. This character might be depicted as a menacing antagonist or, in some cases, an ally. Additionally, characters like Hinata could be main characters as well. Since she has a special relationship with Naruto, she might be involved in the story, either to help Naruto or to be in danger that Naruto has to save her from when dealing with the Flying Dutchman.
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.
Perhaps the Flying Dutchman has a powerful magical artifact on board that Voldemort wants to get his hands on. Harry Potter then has to race against Voldemort to reach the ship first. The ship's ghostly nature could pose a challenge as normal spells might not work as expected on it. For example, 'Apparition' might be disrupted near the ship due to its otherworldly magic.
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.