Chapter 12: To Cut, or Not To Cut Tenjin suggests that Yato cut his ties with Hiyori. Bishamon is estranged from her Ha-clan shinki. Yato and Yukine take a job helping a baby fall asleep, and discover a mask.
Chapter 14: Her Memories Kugaha and Kazuma discuss how they think Bishamon should carry herself. Yato avoids Hiyori, and Yukine meets Suzuha, who tells him the story of Tomoko. Kugaha meets Suzuha under his sakura tree that night.
Chapter 15: That Which Withers Away Yato, Yukine, and Hiyori meet under the sakura tree. Bishamon realizes Suzuha is the name that disappeared, and her shinki continue to hide their sadness from her. Aiha blights Bishamon and Kugaha helps her hide it. Kugaha confronts Yato under the sakura tree.
Chapter 16: Hell Hiyori makes a promise to never forget Yato. Kugaha tells Bishamon that Kazuma partook in Yukine's purification. Yukine finds out Suzuha died, and hitch hikes with Kazuma to Bishamon's estate in Takamagahara. Realizing his betrayal, Bishamon exiles Kazuma.
Chapter 17: In Search of A Place to Go Bishamon's other shinki realize they're weaker without Kazuma to help during battle. Kugaha reveals to Nora his plans to force Bishamon's reincarnation. Kugaha kidnaps Hiyori (her soul only) and Kazuma.
Chapter 18: Drawn Swords Kazuma tells Hiyori why Bishamon hates Yato. Kazuma realizes that Kugaha's plan was to trick Yato into thinking Bishamon had kidnapped Hiyori and cause them to fight. Kugaha threatens Aiha when she questions his plan to reincarnate Bishamon. Tenjin sends Yato and Yukine to Takamagahara, and their face off with Bishamon begins.
Chapter 19: Prayer A deeper flashback of the Ma-clan's extinction is shown while Bishamon and Yato fight. Yukine/Sekki throws himself in front of Yato, and he is broken in half by Bishamon.
Chapter 20: Prayerful Oath Yukine becomes a hafuri, and gain new strength in their battle against Bishamon. Hiyori grows weaker, being apart from her body for so long, but she and Kazuma are released by Aiha. Masked phantoms are released into Bishamon's estate.
Chapter 21: Don't Go—Stay With Me Bishamon suffers from more and more blight. Hiyori clears the misunderstanding, but Bishamon continues to fight until she accidentally injures Kazuma. Ha-clan shinki are killed off by Kugaha's masked phantoms.
Chapter 22: What Must be Done Kugaha explains his reincarnation plans. Yato threatens to kill him, but is stopped by Bishamon. She releases Kugaha and goes to slay the remaining phantoms on her estate. Upon returning, Tenjin reminds Yato that he must cut ties with Hiyori.
Chapter 23: Guiding Light An extensive flashback is shown about Kazuma's entry into the Ma-clan and the discord that led to their eventual corruption and demise. Bishamon tries to become closer with her current shinki. Yato tells Yukine that they're cutting ties with Hiyori.
Chapter 24: Always The main trio, Bishamon and her shinki, Kofuku, Daikoku, and Tenjin and his shinki have a picnic under Suzuha's sakura tree. Kazuma tells Hiyori about masked phantoms. Hiyori decides not to let Yato cut ties with her, despite Tenjin's advice.
- Chapter 14 is spread across two episodes of Noragami Aragoto.
- In the manga, Yukine and Suzuha meet during the daytime and talk until they part shortly before sunset. They also introduce themselves (and the gods they serve) and talk about their experiences as shinki before Suzuha shows him the sakura tree and tells him the story of Tomoko. When they part, Kugaha's presence nearby is hinted at through a depiction of the bells he wears in his hair, but he himself is not shown. This all occurs on the same day.
- In the anime, they meet during sunset nearby the tree, and they introduce the gods they serve while walking away from it. Instead of running away when Suzuha says he works for Bishamon, Yukine stands with a shocked expression and asks, "Seriously?" which Suzuha confirms. Kugaha is then shown hiding behind the sakura tree, smirking while he holds a mask. After Yukine tells Yato about Suzuha, they meet on another day in the same place. This time, Suzuha shows him the sakura tree and explains his history with Tomoko.
- OVA 2 is adapted from chapter 24.