One idea could be that Harry, as Voldemort's soulmate, tries to use their connection to redeem Voldemort. He might show Voldemort memories of love and kindness in an attempt to change his dark ways.
Another plot could be that Voldemort initially tries to use their soulmate connection to his advantage, like getting closer to Harry to find a way to defeat him once and for all. But as time goes on, he starts to have unexpected feelings for Harry that he doesn't understand and that begin to change him from within.
In some fanfictions, the soulmate marks might be used to show a hidden connection between them that goes beyond their enmity. It could be a way to explore the concept that they are two sides of the same coin. The marks could also be a source of power for both of them, either by enhancing their existing magic or unlocking new abilities that are only accessible when they are in close proximity to each other.
A simple plot idea is that the Boggart - Voldemort becomes so powerful in its manifestation that it starts to physically interact with the real world. Harry has to figure out how to stop it before it causes real damage. Another idea is that the Boggart - Voldemort begins to target Harry's friends one by one, using their worst fears against them. Harry then has to find the strength to face his own Boggart - Voldemort to save his friends. Also, what if the Boggart - Voldemort was actually being controlled by a new, hidden enemy? Harry would have to uncover this mystery while also dealing with his fear of the Dark Lord.
One plot idea could be that they discover they are mates due to a powerful magical bond. They then have to hide this fact from the wizarding world which is in the midst of a war. Harry might try to convince Voldemort to abandon his dark ways, using their newfound connection as a way to appeal to his better nature.
One idea could be that Harry discovers a new spell that can penetrate Voldemort's dark magic defenses and uses it to shoot him. Another could be that Harry teams up with some unexpected allies, like the house - elves, who help him get in a position to shoot Voldemort. Maybe Harry has to sacrifice something important, like his invisibility cloak, to gain the power needed to fire the shot that will defeat Voldemort.
One interesting plot idea could be that Harry discovers a new and ancient magic that gives him an unexpected edge in the duel. For example, he might find a spell that can temporarily freeze Voldemort's dark magic, allowing Harry to strike. Another could be that Harry has a vision during the duel that shows him the true source of Voldemort's power, and he uses this knowledge to target it directly. Maybe it's a hidden object or a bond with a dark entity that Harry manages to sever, weakening Voldemort.
One idea could be a story where Bellatrix has a moment of doubt about Voldemort's methods. Maybe she starts to see the destruction he's causing and has to decide whether to stay loyal or turn against him. And Harry Potter could somehow be involved in this internal struggle of hers, perhaps by showing her a different path through his own actions and values.
Maybe Harry absorbs Voldemort and then has to deal with the internal struggle of Voldemort's thoughts within his mind. He constantly battles Voldemort's voice, which tries to persuade him to use power in a wrong way. But Harry uses his own strong will and the love he has for his friends and family to overcome it.
One plot idea could be that the female Voldemort has a change of heart. Maybe she starts to see the error of Voldemort's ways after interacting with Harry Potter. She could start to secretly help Harry and his friends against the Death Eaters, which would create a lot of internal conflict within the Dark side.
One idea could be a fanfiction where Voldemort has a change of heart due to some ancient magic. Maybe he discovers a spell that shows him the true consequences of his actions and decides to work with Harry to fix the wizarding world instead of destroying it.
One idea could be that Harry, influenced by dark magic, forms an uneasy alliance with Voldemort. They could team up to take over the wizarding world in a different way than Voldemort originally planned, perhaps by ruling jointly. Another plot could involve Harry exploring the darker aspects of his own magic and using some of Voldemort's knowledge to do so, which causes a rift between him and his friends.