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In [[4.22 Lucifer Rising]], Dean is taken by the angels to [[Green Room|a safe structure]] where he is held and monitored by [[Castiel]] and Zachariah. Dean eventually figures out that Zachariah has been in favor of the breaking of The 66 Seals that bind Lucifer to Hell all along. After pleading and begging for help, Castiel helps Dean by temporarily banishing Zachariah and teleporting Dean to stop Sam from killing Lilith, as her death is the last seal. Sam ultimately kills Lilith, releases [[Lucifer]], which triggers the [[Apocalypse]] and alerts the Four Horsemen.
Soon after the breaking of [[The 66 Seals]] and [[Archangel Lucifer]]'s release from the Cage, Zachariah and two angel assistants approach [[Dean]] and [[Sam]] at Chuck's house in Kripke's Hollow. Zachariah demands that Dean comes with them but Dean activates a angel banishing sigil, which sends them away temporarily. Zachariah later uses Chuck and lures the Winchester brothers to their father's lock-up in up state New York where he reveals to Dean that he is [[Archangel Michael]]'s Sword wherein he is the true vessel but Dean must first consent to possession. After denying angelic-possession by Michael, Zachariah starts torturing Dean and Sam but Castiel mysteriously returns from the dead and orders his superior away. He inscribes angelic runes into Sam and Dean's ribs which will hide them all angels, including Lucifer and himself.
Sometime later in [[5.04 The End]], Zachariah finds Dean through fringe Christian groups and sends Dean five years into the future (2014). Zachariah appears and says that he wants Dean to see what will result if he continues to resist Michael. At the end of the episode, Zachariah prepares to take Dean hostage but Castiel intervenes and saves him.