The Darkness (Amara) and Chuck revealed as God
15 episodes of Supernatural carry this thread, 15h in all — 14 of them are in The Essentials.
Arc membership is derived from each episode's own summary text, gated to the seasons the sources place each arc in. It shows where a thread is foregrounded, not every episode it touches.
In airing order
After the Darkness passes over them, Sam and Dean wake up and Dean realizes that he encountered the creature at the heart of the storm. Meanwhile, Castiel prays to Heaven to help him, and Crowley takes steps to avoid Castiel.
While Sam tries to find a cure for the Darkness virus invading his body, Dean takes Jenna to her grandmother's. Meanwhile, the angels torture Castiel for Metatron's information, and Crowley learns of the Darkness.
When the Winchesters learn of demons killing witches, they approach one and have her find them Rowena so that they can have her cure Castiel. Meanwhile, Crowley raises the young Amara in Hell but soon discovers that the Darkness may be beyond his control.
Sam and Dean battle a part-vampire/part-ghoul creature that is trying to raise an army to fight the coming Darkness. Meanwhile, Sam receives another cryptic vision, and the Impala witnesses everything.
Sam and Dean track down a double axe-murder at Lizzie Borden's home, and soon realize that something supernatural is involved. As they continue their investigation, they soon discover that Amara is responsible for creating an army of soulless killers.
Sam and Dean get a lead on Amara's location, and try to break in to Crowley's stronghold to kill the embodiment of the Darkness. Meanwhile, Castiel tracks down Metatron and finds him in sorry straits.
While Sam enters Hell with Crowley and Rowena to confront Lucifer and seek his help defeating Amara, Dean investigates the scene of Amara's recent killing and discovers that she has plans for him.
Lucifer takes Sam on a trip through Sam's memories to convince him to agree to possession. Meanwhile, Castiel goes to determine if Amara is dead, and Dean and Crowley come up with a plan to send Lucifer back to his cage.
The Winchesters launch a desperate attempt to recover an artifact capable of destroying Amara by sending Dean back to 1943 to recover the Hand of God from a doomed submarine. They're unaware that Castiel--secretly Lucifer--is the one who must send Dean back through time and return him.
Sam and Dean take a break from looking for Amara to check out a case of a girl going into a coma. They soon discover that their case is connected to a similar case that Bobby and Rufus investigated several years ago... and never completely solved.
Sam and Dean try to convince Crowley to turn over the Horn of Joshua before destroying Lucifer--and Castiel--rather than after they use the Horn to defeat Amara. Meanwhile, an unexpected ally helps Amara heal from her injuries, and Lucifer makes the angels in Heaven an offer they can't refuse.
The brothers investigate a murder-suicide in Colorado that may be tied to Amara. Meanwhile, Metatron receives a request to edit a new book.
Sam and Dean try to come up with a way to rescue Lucifer and discover Chuck's plan to deal with Amara. Meanwhile, a new Prophet is awakened, but he's less than thrilled at the promotion.
To defeat Amara, Sam and Dean will first have to help Chuck and Lucifer reconcile. Once they do, they then must gather the forces of Heaven, Hell, and Magic to weaken Amara so that Chuck can defeat her. However, everything doesn't go quite according to plan.
It's the end of the world as Chuck's death extinguishes the sun. Desperate, the Winchesters, Castiel, Crowley, and Rowena come up with a plan... but to succeed, one of them will have to die.