After his defeat and Heaven being reclaimed by the angels, the Scribe of God Metatron was locked away in Heaven's dungeon. In a desperate attempt to find a cure for the Mark of Cain, Metatron is broken out by Castiel, Sam Winchester and Bobby Singer. In order to leverage Metatron for the cure he claims to know, Castiel removes Metatron's grace and renders him human. Metatron turns out to not know of a cure for the Mark of Cain, but offers to take Castiel to the remainder of his grace if Castiel won't kill him. Castiel is able to get his grace back, but Metatron stuns him and escapes with the Demon Tablet. While Metatron is able to avoid recapture, the Winchesters and Castiel begin searching for him with more earnestness following the release of the Darkness, believing that Metatron might know something helpful about the Darkness and how to defeat her.
While watching the nightly news, Castiel sees a video of a homicide in Omaha, Nebraska where the cameraman is Metatron. Castiel manages to get Metatron's address from the TV studio and locates the demon tablet beneath his mattress. Castiel then scours the police scanner and learns of the location of a shooting and heads there, believing Metatron will attempt to get there before the authorities and record it.
At the scene of the shooting, Metatron records the gun used and the victim and is pleased with the fact that he will get at least five hundred dollars for the footage. Stating that he still needs more money, Metatron robs the victim who turns out to be mortally wounded, but still alive. Metatron is annoyed as he would get more money if the man was actually dead and in response to the man's pleas for help, tells him that there was a time when he could've brought the man back from the brink of death, but isn't that guy anymore. At that moment, Castiel arrives, shocking Metatron and explains how he found Metatron. Castiel heals the man's wounds as Metatron records it. Seeing this, Castiel smashes Metatron's camera out of his hand to his annoyance and leaves with him as a police car arrives to help the formerly-wounded man.
Castiel takes Metatron to an abandoned warehouse where Castiel expresses his disgust for how Metatron preys like a vulture on injured and dying people. Metatron tells Castiel that after Castiel took his grace and left him human, he was left with nothing and was on the run from angels but built a life for himself. Metatron claims that reality is the new literature and he is now reality's author. Castiel stops Metatron's explanations and starts to question him about the Darkness, but Metatron misunderstands Castiel to be asking about the demon tablet. Metatron quickly lies that he hid the demon tablet where Castiel where never find it, but Castiel simply pulls the demon tablet out of his pocket and explains how he found it, annoying Metatron that Castiel broke into his apartment. Castiel asks Metatron what he knows about the Darkness and while Metatron admits that God told him something, he refuses to say what. When Castiel tries to threaten him, Metatron taunts him, stating that he can tell that Castiel is broken and paralyzed with fear and trauma. As Metatron taunts that Castiel can't even bring himself to hit him, Castiel attacks, beating Metatron. As Castiel continues to demand information on the Darkness, Metatron taunts Castiel about his state and Metatron's role in it. Finally, Metatron orders Castiel to kill him and Castiel stops himself, realizing Metatron was manipulating Castiel to kill him.
Metatron begs Castiel to help him and explains that he can't stand a human life, finding it too hard and undignified. Castiel tells Metatron that Metatron is right that Castiel is tired of being manipulated and thus he won't allow Metatron to manipulate him into letting Metatron off easy. Castiel asks about the Darkness again and Metatron finally tells him that to make Creation, God had to sacrifice the only kin he ever had: the Darkness who is his older sister.
After getting what Metatron knows out of him, Castiel chooses not to kill or imprison him again, seeing him as harmless as a human and "pitiable" now. Instead, Castiel lets Metatron go though he later tells the Winchesters that he left Metatron in traction.
After reuniting with the Winchesters, Castiel informs them of what he learned from Metatron along with the fact that he let Metatron go. Dean is less than pleased by this, but Castiel stands by his decision as he sees Metatron as pitiable and no longer a threat.
- This is the final time the Winchesters or Castiel come into conflict with Metatron. Upon his return in Don't Call Me Shurley and All in the Family, Metatron aids them by convincing God to come back and sacrificing himself to help rescue Lucifer.
- In a deleted scene for Don't Call Me Shurley on the season 11 DVD, Metatron admits he deserved the beating Castiel gave him and explains that the feeling of mortality he experienced following waking up in the hospital after the beating was what caused him to change his view on humanity.