In some fanfictions, Voldemort wins through a change in the prophecy's interpretation. If the prophecy was misread, it could give him an edge he didn't originally have.
In many WBWL fanfictions where Harry is powerful, he often uses his hidden powers to resist Voldemort's regime. For example, he might have an extraordinary control over magic that was suppressed in the original story. He could use this power to secretly help the resistance, like teaching other wizards and witches how to fight against the dark arts in new and unexpected ways.
One reason could be his pure heart. Harry's pure intentions and lack of desire for power for power's sake gives him an edge. His magic is not corrupted like Voldemort's. It flows more freely and is more in tune with the natural order of magic. So, when he casts spells, they are more effective.
Harry may show greater power in his connection to the magical world around him. He has always had a special bond with Hogwarts. In the fanfiction, this bond could be enhanced. So, when Voldemort tries to attack the school, Harry is able to draw on the magic of Hogwarts itself. He can use the ancient magic stored within the castle walls to create powerful shields and offensive spells that are far more potent than anything Voldemort can muster.
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.
Well, in such fanfiction, Voldemort's possessiveness might show through his constant attempts to control Harry's actions. He may try to isolate Harry from his friends and allies, wanting Harry all to himself in a very dark and twisted way. For example, he could use dark magic to keep Harry in a certain place or manipulate situations so that Harry has no choice but to be near him.
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.
In some fanfictions, Voldemort might save Harry due to a complex change in his character. For example, he could discover a newfound sense of respect for Harry's power or courage. Maybe he realizes that Harry is the only one who can truly understand him, and in a moment of strange kinship, he decides to save Harry from a greater threat that is about to befall them both.
Maybe Harry uses some powerful and unexpected spells. For example, he could combine the Patronus Charm with a blasting spell. The Patronus might distract Voldemort while the blasting spell hits him hard.
Often, Voldemort starts as this purely evil figure. But when he adopts Harry, he begins to show some unexpected softness. For example, he might start to protect Harry from other threats, which is very different from his usual self.