I don't own Haven and never will. No copyright infringement intended.
William knew Audrey long before she was Audrey. Back then, the Troubles didn't exist and they were relatively happy. Sure, it had been an arranged marriage, but William fell in love with Elizabeth. She was perfect for him. And she hadn't felt the same way at first, but her feelings had changed before everything was shot to hell.
The town changed out of the blue one day. People started dying for odd reasons. Supernatural powers were used by many when they had previously been fine. Others claimed witchcraft, but when the Troubles (a name Elizabeth came up with) affected them, they changed their tune. Elizabeth tried to help, bless her, and it worked.
And then some man named Howard came and told Elizabeth she had to leave with him - it was important. She agreed, angering William, but she refused to listen to him. Elizabeth wanted the Troubles to end and for innocent people to stop dying. It's why she dug her heels in. So William, even though he had a Trouble of his own (which he gleefully used), followed her into the Barn. He didn't want her to be alone if he could help it.
He watched her leave every twenty-seven years as someone else to help the Troubled and waited for his chance to remind her of who she once was. The opportunity finally arose when the Barn started dying and Lexie became the new personality. She trusted him. It was what he wanted.
William will get his Elizabeth back and they'll be happy again. They can be what they were before and everything will be normal again. Elizabeth loves him and he knows it. They'll stop the Troubles together (by killing everyone in Haven, of course) and then go off together to live however they want to.