In an alternate timeline caused by [[John Winchester]] getting pulled from 2003, Zachariah arrives in [[Lebanon, Kansas]] with the alternate timeline [[Castiel]] to investigate. Walking into a nearby restaurant, Zachariah demands to know who has been messing with time, causing the patrons to think he's nuts after he claims to be from [[Heaven]]. Zachariah threatens to have Castiel murder them all otherwise and Castiel displays his wings.
The effects of Castiel displaying his wings draws the attention of [[Sam]] and [[Dean]] from outside and they enter the restaurant to investigate and are shocked to find Zachariah. Zachariah is equally shocked to see them, commenting that Heaven had big plans for the Winchesters before their father disappeared. Zachariah quickly realizes that the Winchesters are responsible for what happened and orders Castiel to kill them. As Castiel takes on Dean, Zachariah begins choking Sam, demanding to know what he did. Zachariah taunts Sam, moving closer as he demands that Sam speak. Zachariah doesn't notice Sam draw an [[angel blade]] from his belt as he moves closer. Once Zachariah is in his face, Sam stabs him in the heart with the angel blade, killing Zachariah.
After John is returned to his own time, events return to normal, erasing the alternate timeline Zachariah from existence.