Maybe there's a powerful and corrupt wizard in the Ministry of Magic who doesn't want Harry to have an independent means of travel like the yacht. This wizard could send his minions to disrupt Harry's work, or even create false laws that would make building the yacht illegal in the wizarding world.
One possible plot is that Harry is challenged by a wizarding adversary to a race across the ocean. So, he decides to build a yacht. He enlists the help of Hagrid, who provides some rare magical wood for the yacht. Harry then uses his experience from flying on brooms to design the yacht's sails in a way that it can move extremely fast. The yacht might also have a cabin filled with magical artifacts that help him on his journey.
The Death Eaters could be the antagonists. Even though Voldemort is gone, some of his followers might not want Harry to succeed in building a starship as they fear it could bring more power to Harry and his friends, and they still hold grudges against him.
Ron could also be a great ally. His loyalty and courage would be important. He might be in charge of security, using his skills in wizard chess to plan out defensive strategies. And of course, the Weasley family in general could offer a lot of support, with their various skills and connections in the wizarding world.
Maybe an old wizard who has been secretly studying the combination of different magical universes for years. This wizard could have made some initial attempts at building a lightsaber - like weapon in the past and can share his experiences and mistakes with Harry. He would teach Harry about the balance between the light and dark side of this new form of magic, just like the Jedi teachings in Star Wars.
Obviously, his friends Ron and Hermione would be among the first to join. Neville could also be a key member, as he has shown great courage. Then there might be the members of Dumbledore's Army who are still at Hogwarts. The Weasley twins could also be part of it, using their unique magical inventions to give the army an edge in battle.
Hermione could be a main character. She would use her intelligence and vast knowledge of magic to help Harry plan and build the city. Her skills in research and spell - casting would be invaluable.
The Thalmor could be great antagonists. Their strict control over magic and their anti - human beliefs could put them at odds with Harry. They might see his different form of magic as a threat to their power in Skyrim.
It could be a new dark wizard who wants to make a name for himself. He sees Hogsmeade as an easy target to show his power. He starts by causing small disruptions like making objects in the shops move on their own and then escalates to more dangerous attacks that Harry has to stop.
The Ministry of Magic could be a major antagonist. Since necromancy is considered a dark art, they would try to stop Harry at all costs. They might send Aurors after him or try to expel him from Hogwarts.
Some pure - blood supremacist wizards might oppose Harry. They may not like the idea of a half - blood like Harry having so much control over a city and could try to create unrest. Also, there could be some non - magical criminals who target the city because of its new magical elements under Harry's leadership.