One possibility could be that Harry is the son of a powerful but mysterious wizard and a muggle - born witch who had to give him up for some reason. Maybe his real father was a dark wizard who was hunted down, and his mother was a brave witch who wanted to protect Harry from that dark legacy.
Perhaps Harry was created through some magical experiment. His 'parents' could be a group of powerful wizards who were trying to create a super - wizard. When the experiment went wrong or they realized the implications, they placed Harry with the Potters, but he has no biological relation to them.
He could be the son of a long - lost pure - blood family that had been in hiding. His real parents might have been in hiding from some dark force, and when they were discovered, they sent Harry away to the Potters for protection, but the Potters never got the chance to tell anyone the truth before they died.
If Harry isn't James's son in the fanfiction, it might lead to a different prophecy. In the original story, the prophecy was about Harry as the son of James and Lily. Without that relation, the prophecy could be about someone else entirely or have a different interpretation. Also, Voldemort might not target Harry in the same way. He targeted Harry because of the threat he posed as the son of James and Lily. This could lead to a very different power struggle in the wizarding world, with other characters coming to the forefront as the main targets or heroes.
In some fanfictions, it could be Sirius Black. Some fans like to imagine that Sirius had a deeper connection to James Potter's family than just being best friends. They might create a scenario where there was some sort of magic or prophecy involved that made Sirius more than just Harry's godfather, but his actual father in this alternate story line.
There could be old friends from their school days. For instance, a classmate who knew some deep secrets about them. Maybe this friend was also in the same secret club or society that his parents were part of, and after their deaths, this friend tried to keep an eye on Harry from the shadows.
Well, it could be two powerful Aurors who were thought to be dead but were actually in hiding. They might have been fighting against Voldemort's forces and had to disappear to protect their family. Maybe they were friends with James and Lily Potter and got caught up in the same battle that led to the Potters' death.
Well, it could be a very peaceful setting. They might be looking down on Harry and feeling proud of all he has accomplished. Maybe they're reunited with their friends who also passed away. They could be having long conversations about the wizarding world and how it has changed since their time.
In some fanfictions, Sirius Black is sometimes portrayed as Harry Potter's real father. This idea might stem from Sirius's deep connection and loyalty to Harry, as well as his role as a father - like figure in Harry's life.
Apollo could be Harry's father. Apollo is the god of music, poetry, and prophecy among other things. If Harry was Apollo's son, he could have an innate talent for divination that is far beyond what he showed in the original books. He might also be able to use music as a form of magic, perhaps charming his enemies or healing his friends with melodies.
It could be Athena. She is known for her wisdom, and Harry has shown great intelligence throughout the series. Maybe his strategic thinking and ability to solve complex problems come from his connection to Athena.
Hermione would definitely be one of his top allies. Her intelligence and knowledge of magic and history would be invaluable in helping Harry rule. She could advise him on laws and policies, especially those related to education and the treatment of non - human magical beings. Ron would also be an ally. His loyalty and his understanding of the wizarding world's less - sophisticated side could help Harry connect with the common wizards.
Hermione would be a likely colleague. She's highly intelligent and could be teaching a subject like Ancient Runes or Arithmancy. Ron could also be there, perhaps as a flying instructor or teaching something related to magical creatures. Neville might be a Herbology professor, given his love and talent for that subject. Luna could be teaching something really unique, like the study of magical creatures that are often overlooked or misunderstood.