Sean Flynn acted as the vessel for the angel Josiah.
Sean was a resident of Omaha who assented to possession by the angel Josiah, a follower of Castiel. When Josiah failed to attend roll call, Hannah suspected he was the a mole as his disappearance coincided with the death of Ezra.
Sam and Castiel manage to track Josiah to Pray, Montana. They discover a warehouse they initially assume is the doorway to Heaven, but inside they find Josiah badly burnt. The angel had been tricked to this location by Metatron and got dossed in Holy Oil. He refuses to be healed by Castiel so he doesn't owe his life to what he does not see as a real angel.
Josiah's decision leads, indirectly, to Sean's death as well.