After the escape of Amara, the Winchesters inadvertently help Lucifer escape the Cage and he possesses Castiel. During an attempt to free Castiel from Lucifer's control, he is captured by Amara who begins torturing Lucifer to try to force God out into the open.
After being brought to God to help finish his autobiography, Metatron convinces God to help in the struggle against Amara. However, Metatron also learns that God intends to sacrifice himself to Amara in an attempt to get her to spare the universe. In an attempt to stop this, Metatron contacts the Winchesters and offers his help in anyway he can so as to save God and his creation. The Winchesters accept Metatron's help and enlist his aid in rescuing Lucifer so he can help God defeat Amara.
Having been contacted by Amara, Dean agrees to meet with her in a forest as a distraction to allow Sam and Metatron to locate Lucifer with the help of the Prophet Donatello Redfield. Amara thanks Dean for reaching out to her, saying she misses him and the sensations he arouses in her. Dean tells Amara that there can't be a them and they should just walk away, leaving her to wonder why he doesn't. Amara tells Dean that God can't stop her again and suggests that he give up his humanity and become "boundless" within her. Dean admits that he is drawn to Amara and it bothers him as he can't control it. Amara questions why Dean fights it when he knows she is the end of his struggle. As Amara touches Dean's face, she realizes she can't read his thoughts and something is different. Amara realizes that Dean has spoken with God and has betrayed her and departs to stop Lucifer from being rescued.
At the same time Dean meets with Amara, Sam, Metatron and Donatello locate Lucifer in an old grain silo. Lucifer mocks them and tells Sam that the least they can do is to rescue him since they are the reason he's there. Sam tells Lucifer that if they rescue him, he has to help them take down Amara and if he refuses, they will leave him behind for Amara. Lucifer is enraged that Sam would imply that he wouldn't help them after what Amara has done to him. As Metatron recites a spell to release Lucifer, Sam tells him that he will have to work with his father. Lucifer agrees to table his problems with God as dealing with Amara is bigger than that. Metatron is eventually able to free Lucifer but he is too weak to teleport them out.
As they try to figure out what to do, Donatello senses that Amara is coming. As Sam and Donatello leave with Lucifer, Metatron stays behind, telling Sam to go and that "I got this." As Sam, Lucifer and Donatello flee in the Impala, Metatron cuts his hand and draws an angel banishing sigil on a table. Moments later, Amara appears, and Metatron attempts to use the sigil to banish her to no effect. Metatron tells an amused Amara "He meant well. Spare the universe" but Amara simply surrounds him in darkness and implodes Metatron into nothingness.
After Sam, Lucifer and Donatello arrive in the Bunker, God tells them that he sometimes does answer prayers and he and Lucifer greet each other. God then heals Lucifer's injuries from Amara's torture. Dean later expresses his surprise to Sam that Metatron sacrificed himself to save them.
- The death of Metatron while rescuing Lucifer is the first death of a Big Bad, or former Big Bad in this case since Abaddon's death two years earlier. Metatron was co-Big Bads with Abaddon but was defeated and not killed.