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According to Ion, Naomi and himself are from the intelligence division in Heaven.After Castiel has reunited with the Winchesters and rescued the prophets from Crowley – as well as splitting the Word of God tablet in two – he is summoned to Naomi, who reveals her role in saving him and asks him to tell her about the Winchesters' recent progress.
After learning that Samandriel revealed the existence of an angel tablet, Naomi orders Castiel to kill him which he does against his will.She was responsible for rescuing Castiel from Purgatory – although it cost several angels their lives to recover him – and has continued to monitor him.It is implied that she had a past fling with Crowley in Mesopotamia.Crowley starts to offer her a deal, but she disappears instead, annoying him as he usually disappears like that.Later, Naomi is seen in Heaven being reported to by another angel on the lack of luck they are having in the search for Castiel and the tablet.Naomi meets with Dean in Garth's houseboat after Sam has gone to Hell to rescue Bobby Singer and complete the second trial to close the Gates of Hell.
Naomi tries to convince Dean that they are on the same side, telling him that she did meet with Castiel periodically but wasn't having him spy on them and that he misinterpreted her orders to protect the tablet at all costs as meaning to kill Dean.
After the Winchesters break the Enochian sigils keeping him out, Castiel is still left weakened and as an apparent side-effect, sees a memory of Naomi having him strapped down to a chair and approaching his eye with some kind of instrument.
After Samandriel is rescued, he begs Castiel to not take him back to Heaven as he is afraid of Naomi after what he has revealed.
After Castiel encounters the Winchesters during his search, Naomi has him lie to them, telling them that he is searching for Crowley's half of the demon tablet while the demons are searching for a parchment that will allow them to translate their half of the tablet without a prophet.
When the demon Castiel is torturing is about to reveal the truth, Naomi has Castiel kill her with his angel blade.
Naomi claims Castiel is still broken and wants to save him.