Nathaniel is an angel who worked for Naomi in the Intelligence Division of Heaven up until the point all angels were expelled from Heaven by Metatron.
Nathaniel enters Naomi's office in Heaven to report to her the news of one of their freelance operatives having spotted Castiel in Houston, Texas. He also tells her that spotted alongside Castiel as well is Metatron which shocks Naomi upon hearing the news. She then dismisses Nathaniel and he is not seen again however he was most likely one of the many angels expelled from Heaven by Metatron falling to Earth.
Nathaniel in Lore
In angel lore Nathaniel (also known as Xathanael and Zathael) is known as an archangel, whose name means "Gift of God." According to Judaism he is the sixth created angel, and one of the twelve angels of vengeance. Nathaniel is also said to be the angel of purification, divinity as well as fire - holding dominion over the element, which is seen as a powerful gift from God. Other lore stats him as one of the three angels who have patronage over all things hidden, mysterious, or arcane.