His wife left him, but in the dub this was changed to her disappearing when looking for Unown, a project he was a part of as well. One day, as he explored an ancient building with his assistant Schuyler, he too vanished into the alternate dimension of the mysterious creatures after discovering a chest full of stones with the Unown carved on them. His daughter was sad because he didn't return, so the Unown created an illusionary Entei to be her father in Spencer's stead.
He remains in the Unown's dimension until the end of the film, when, after Entei breaks through the barrier and the Unown were no longer out of control, the Unown return to the ruins from where they originated, which allowed Spencer Hale to be free from the dimension. He returned later, as did his wife, after the Unown's influence over Molly ended.