If they joined Voldemort, the story would go off in a very different direction. Harry might be able to learn more about the Dark Arts directly from Voldemort, which could either corrupt him completely or give him some unique knowledge to use against Voldemort later. Fred and George would likely face a moral struggle. Their loyalty to their family and friends would be tested, and they might try to find ways to protect those on the side of good while seeming to be on Voldemort's side in the fanfiction.
If they joined Voldemort, Harry might lose some of his natural courage. He'd be in a world where his usual values are flipped, and this could make him seem more hesitant. Hermione would probably have to hide her intelligence more. Voldemort doesn't like those who are too smart or independent. So she might act more subservient in public, but in private, she'd be devising plans to break free and expose Voldemort's true nature.
The plot could develop in a number of ways. For one, Voldemort might use Harry as a symbol to further his control over the wizarding world, claiming that even the 'Chosen One' has seen the error of his ways and joined him. Fred and George could be used to spread fear and chaos with their magical skills, but they might also try to use their position to gather intelligence for the resistance. Another aspect could be the reaction of the other characters. Hermione and Ron would be devastated and likely try to find a way to rescue their friends. The Order of the Phoenix would have to reevaluate their strategies completely.
Perhaps Voldemort discovers that there is a greater threat out there. In the fanfic, it could be that another dark force is emerging, and Voldemort sees Harry as an ally of sorts against this new threat. So, he decides to protect Harry in order to deal with this common enemy.
It could be a time-travel or alternate universe fanfiction. Maybe Harry's soul gets swapped with Voldemort's or there's some magical curse that changes his identity.
After Harry kills Voldemort in the graveyard in the fanfiction, the magical balance might shift. With Voldemort gone, some of the dark magic that was prevalent might start to fade away. The Hogwarts School of Witchcraft and Wizardry could see a new golden age. New spells and magical theories might be explored as the fear of Voldemort no longer holds back the wizarding scholars. Harry himself might start to travel around the world to spread the news of Voldemort's defeat and also to learn more about different types of magic. His friends would also have new opportunities, like Hermione might be able to further her studies without the constant threat of Voldemort and Ron could finally relax and enjoy a more peaceful life at the Burrow.
One possible scenario is that Harry masters a new and powerful form of magic that Voldemort has been unable to attain. For instance, if Harry discovers a way to combine different branches of magic in a unique way that gives him an edge in battles. Voldemort, who has always been obsessed with power and being the most powerful wizard, would surely be jealous of Harry's newfound abilities.
Harry often becomes more conflicted. He has always seen Voldemort as the ultimate evil, but now being mates, he has to re - evaluate his views. He might start to see the humanity in Voldemort, which makes him question his own beliefs and actions in the fight against the Dark Lord. For example, he may hesitate in battles more than before.
Often in fanfiction, their relationship can change drastically. They could end up as allies, which would require both of them to change. Harry would have to see past Voldemort's evil deeds, and Voldemort would have to let go of his hatred for Harry. This exploration of character change makes fanfiction so interesting.
The wizarding world might be in shock. People who have always seen Voldemort as the ultimate evil would be confused. They would have to re - evaluate their views on Voldemort. Harry, on the other hand, would be in a very strange situation. He might be distrusted by some of his friends who think he has made a deal with Voldemort.