Note: This story includes infidelity on the part of two beloved characters, in part due to the fact that divorce is not an option. However, those who are particular about that may wish to look elsewhere. None of these characters are perfect, and they often make bad decisions with consequences.
Hermione had never believed in soulmates, even after listening to her parents tell the story of how their eyes had met across a room at a dental convention. She was too logical when she was young. It was so illogical. Like something out of her mother's romance novels that she kept on the highest shelves. When she discovered that magic was actually real, she took a bit of an academic interest, but there were few mentions anywhere academic. The best sources she could find were the wizarding equivalent of her mother's romances, hoarded by Parvati and Lavender and discussed in whispers. Hermione rolled her eyes and filed it with Divination as mostly nonsense and self-fulfilling prophecy. She refused to believe there was only one boy in the world for her.
She thought about it briefly in fourth year when Viktor Krum walked duck-footed into her life, but he sailed away just as quickly and any stirrings she may have felt were quickly pushed into a box labelled friendship. She was still so young, after all, and everyone knew long-distance relationships didn't work.
When she came to terms with the fact that she had feelings for Ron she never even considered the concept. Everyone else did, commenting on how they had been like an old married couple for years, but she knew better. Their friendship took work, compromise and broken rules. It wasn't easy, why should she expect a romance with him to be easy? She did love him, she just loved him with both eyes open and sometimes filled with tears, like when he was with Lavender or when he abandoned them on the horcrux hunt.
When she and Ron had finally said I do, it was one of the happiest days in her life, one of the few times since the war that she honestly felt at peace and happy. They were happy for almost a year before it all started to fall apart and Hermione discovered that there was no such thing as divorce in the magical world - not even when your best-friend-turned husband-turned-Auror-turned-shopkeeper-turned-Quidditch-player cheated on you. That was the third worst day in her life.
The second worst was miles away from their flat, when despite her general dismissal of the concept, she discovered a soul bond in a flare of magic that made her weak in the knees.
And the absolute worst was the day she made a decision and walked away from the two most important people in her life. The soul bond was important, but she loved Ron without magical bonds being pushed on her, and he had found her parents. How could she ignore such an act of devotion from a man who could have any Quidditch groupie? Abandoning England and Ron also meant abandoning Harry, her newly discovered parents, and everyone else she had cared about since she had gotten a visit from Professor McGonagall. She had chosen the marriage bond, the soul bond chose her, and she would cherish it in the depths of her heart forever, but she had already made her choice when she didn't know she had a choice.
So, she chose her marriage and her heart broke.