In the alternate timeline, DS fails to control Giratina when the Legendary appears to confront Cyrus. Giratina's power is left to run amok as Cyrus takes control over the legendaries Dialga and Celebi and uses them to overpower even Giratina, and then the other Legendaries. DS herself is rescued by Cynthia.
As a result of Giratina's power and Cyrus's interference, Mt. Coronet first and Sinnoh later start getting engulfed in a dimensional distortion that grows over the region, eventually rendering it pretty much unfit for human habitation until it is restored following the events of the AU arc. In the future that ends up becoming PMD-B, Sinnoh is more or less a remote wildland where not even the Sinnoh Cubone Tribes inhabit, having moved elsewhere as a result of the dragons forcing them from their original home.