Just as predicted, the mysterious barn returned and the Colorado Kid emerged from it along with Audrey's former boss, Agent Howard -who obviously never worked for the FBI, but is connected to Haven somehow.
Agent Howard told her if she herself went into the barn, "The Troubles" would end for another 27 years. Seeing this as the lesser of two evils, Audrey kissed Nathan goodbye and went into the barn - with Duke unexpectedly jumping in after her. A distraught Nathan shot Agent Howard and the barn disappeared.
Arla ended up accidentally killing The Colorado Kid, so his plan to allow Audrey to kill him (and end "The Troubles" forever, because he was kinda sorta her son and thus she loved him) failed. So Audrey's only choice to end "The Troubles" is to kill another person she loved - Nathan. She refused.