While fighting Ragna as the Black Beast, Noel Observes the Gate to the Azure. If she opens it, she knows it would end the world, so she separates herself into two beings: Noel and Mu. Noel has no Godslayer abilities and is missing many memories. Mu is able to revert the Black Beast back to Ragna. Jin is critically injured during the fight and loses his memories of it.
Kokonoe tells Kagura, Tager, Makoto, and Hibiki everything she knows about Ragna.
Jin talks to Noel to try to find out what happened during the fight with Ragna. Noel doesn't remember much more than Jin. Rachel also tries to make Noel remember, but fails.
Jin talks with Trinity, who is now residing in Yukianesa. She tells him she made it so Hazama and Terumi can't fuse again, but Terumi is still at large. She asks for Jin's help in finding Platinum so Terumi can be defeated. In return, she offers the bedridden Jin a new body without any injuries. Jin agrees to help her.
Izanami teleports Rachel and Noel to her. Izanami says it's time for the qualified (sometimes translated as Entitled or Chosen) to battle.
Almost all of the people in the world have become Seithr and are absorbed by the Embryo. Those with strong souls can move freely and are called the 'Chosen.' The Origin creates a world within the Embryo and most of the cast's memories adjust to fit the world that was created. Jin, Trinity, Hakumen, Rachel, Celica, Nine, Izanami, and Hazama retain their memories. Ragna is not Chosen, but he is able to exist in the Embryo anyway. Platinum can not substain their body in the Embryo. If a Chosen obtains the Azure, they can recreate the world to fulfill their dream. If no Chosen obtains the Azure, then Doomsday happens: All existence will become Seithr and the world will remain an Embryo for all eternity.
Amane recreates Takamagahara within the Embryo.
Nine is currently working with Relius to end the world. She wants to gather all the Nox Nyctores in order to use their cores to make Take-Mikazuchi whole again. When it's fully powered, it should be able to knock away Tsukuyomi and then destroy the Master Unit. After the Master Unit is destroyed, her cooperation with Relius will end. Then she plans to rewind time and use Take-Mikazuchi's core to complete the 11th Nox Nyctores Requiem, her replacement for the Master Unit that won't make Interventions. Her goal is to protect her loved ones and give them happy lives.
The Embryo recreates the Calamity Trigger period. Ragna doesn't remember anything about himself although he feels some facts, like Kagura being the "Hero of Ikaruga", are wrong.
Naoto lands from another world and travels with Celica in search of Raquel Alucard. Rachel says Naoto is the same existence as Ragna. Relius and Valkenhayn recognize him from their past, but say that he was killed by Clavis. Naoto recognizes Hazama (although Hazama does not recognize him) and many other characters (Makoto and Hakumen) remind him of people from his world.
Ragna eventually makes it to the Kagutsuchi Cauldron where he easily beats Nu. He says he wants to save Nu and offers his hand to her. The world distorts.
Nine summoned Ragna and attacks him. She easily wins. Ragna gets all his memories back. He breaks free from Nine and says he'll save Saya, Noel, and Mu once and for all without killing anyone. Nine tells him the only way he can fulfill his dream is by killing Izanami. Then Nine performs a massive Phenomena Intervention.
Nine uses Requiem to recreate the Chrono Phantasma period. She sends a telepathic message to all the Chosen: They must kill Izanami to make their "dream" come true. This message implies only one person can make their "dream" come true.
Rachel has lost almost all of her powers, but is still determined to help Ragna. She can no longer teleport at all. Valkenhayn says he'll support her cause.
Terumi and Hazama can't fuse unless Hazama touches the Azure to heal the wound Trinity gave him. Terumi really wants to obtain Noel.
Azrael breaks out of his dimensional prison and attacks Izanami. He eventually agrees to serve her by killing the Chosen. In return, he'll be given the opportunity to fight the gods.
Kokonoe and Kagura figure out something is off about the world. They obtain and protect Noel.
Ragna meets Rachel and learns about the Embryo and the Chosen. Ragna fights Azrael, but soon gets warped away by Izanami. Izanami tricks Ragna into killing her. The Origin doesn't like this conclusion and causes an Intervention back to the Chrono Phantasma period.
The Master Unit and Embryo appear within the Embryo. Everyone except for Noel gets their memories back
Ragna learns that the world loops because it reflects the dream of The Origin. Ragna decides to end her dream. If someone else takes The Origin's place, then the world will be back in the same position, just with a different God. Ragna decides to take the dreams of all the Chosen using his Soul Eater and use them to operate the Master Unit. That way, everyone's dreams can come true and there will be many 'possibilities' again.
Ragna meets Hazama, who gives him Mu. Ragna begins collecting the dreams of every Chosen he comes across. Rachel tells Ragna he should accept help with his task, but Ragna refuses.
Requiem causes a Phenomena Intervention that brings the world back to the Calamity Trigger period. Ragna is not deterred, but is having a harder time getting around and containing all the dreams. Requiem causes another Phenomena Intervention, bringing the time period back to Chrono Phantasma.
Jin finds and restores Platinum. Jubei finds Jin's group. He asks Trinity and Jin to help him destroy Requiem. He asks Platinum to use Muchorin to make another Hihiirokane. Everyone agrees to help Jubei.
Rachel, Kagura, Kokonoe, Noel, Jin, Jubei, Celica, Hibiki, and Trinity find Ragna after the last Intervention. Rachel has brought them up to speed and they want to help Ragna. Ragna finally accepts their help. They decide their first task is to destroy Requiem. Everyone except for Kagura and Hibiki need to go to Nine's secret lab, break into her workshop, and destroy Requiem's core.
They make it to Nine's workshop where they find Requiem and Nine waiting for them. Nine tells them about the Prime Field War, how The Origin keeps selfishly rewinding their world, and what Nine plans to do. Ragna's group can't accept Nine's plan to rewind time and deny the present. Ragna fights Nine one on one. During the fight, Nine is distracted by thoughts of Celica. Ragna uses that moment to defeat her. Nine says her goodbyes and says she genuinely hopes Ragna's plan works.
Izanami and Nu come in to kill everyone. Nine says she prepared for this. Nu attacks Nine, but Jubei defends her. Nine dies activating the incomplete Requiem, which has the power to freeze time in the room for a week, thereby imprisoning Izanami. Jubei continues to hold Nu off, which gives Celica time to provide Rachel with enough mana to teleport the group. Celica used too much magic helping Rachel transport them and will shortly fade away. Izanami, Jubei, Nu, and Requiem are stuck in the time freeze.
Rachel, Celica, Ragna, Jin, Kokonoe, and Noel are transported to Celica's church, which is mysteriously restored. Noel finally merges with Mu at the Black Beast's remains beneath the church and regains her memories and powers. Noel realizes that she shares a soul with all her "sisters", including The Origin and Izanami. Noel also realizes she exclusively shares Saya's soul with Izanami. As the group teleports back to Sector Seven, Celica fades away.
Naoto learns his world can be restored if he saves this one. Kokonoe finds Naoto and learns that this is the only world that still exists. Jumping into the Embryo transports you to a new world, but since this is the only world left, you'll always end up back on this world.
Terumi obtains the original Hihiirokane from Alucard Castle. Even though Hazama touched Izanami to repair himself, Terumi chooses not to fuse with him and uses Hihirokane to permenantly sever their connection.
Hakumen and Tsubaki give Jin the Hihirokane that Platinum created. The whole group schemes: Lambda and Tager will guide a group into Nine's frozen lab through the Embryo. Requiem is set to explode and destroy the world, but Minerva will cancel out this explosion by blowing herself up. Hakumen will rescue Jubei. Noel will defeat Izanami by merging with her. Ragna will handle Terumi and the Master Unit.
Izanami was trapped in Nine's workshop, but she wasn't frozen. She used the past week to create a mini-world and bring in Azrael, Hazama, and Terumi. She splits the heroes up into three groups: Kagura/Jin/Trinity, Tsubaki/Hakumen, and Ragna/Noel/Minerva. Rachel is sent to Hazama, who binds and tortures her near a Cauldron.
Kagura, Jin, and Trinity encounter Azrael. Azrael is really strong, but has no technique. Kagura sees through his style and wears out Azrael's stamina. Jin freezes Azrael and Trinity teleports him back to the Sector Seven prison.
Naoto and Makoto enter the Embryo. Naoto listens to Makoto because she reminds him of someone from his world.
Ragna's group finds Izanami and Requiem. Ragna and Noel team up to defeat Izanami. In the end, Noel consumes Izanami. Minerva prevents Requiem from destroying the world by self-destructing herself. The time freeze ends.
The disqualified Chosen start turning into Seithr. Es (the guardian of the Gate to the Azure, an Embryo Storage, and the arbitrator between Azure and Humans) begins visiting all the Chosen. If they reject the Azure, she backs up their souls before they turn into Seithr. If the world is saved, they can be recreated.
Tsubaki and Hakumen find Jubei and Nu, still in battle. Nu has absorbed Take-Mikazuchi and is powerful. Ragna, Noel, and Jin arrive. Ragna easily defeats Nu. Ragna reveals the Chosen's souls are being absorbed into the Boundary and have become weaker. Ragna isn't stronger, everyone who relies on Drives is just weaker.
Terumi reactivates Nu and forces her to fight. Hakumen defends Tsubaki from Nu. While Hakumen is focused on Nu, Terumi uses Hihirokane against him. Terumi takes back his original vessel. Terumi overpowers everyone. He takes Noel and the Master Unit out of the Embryo with him.
Ragna, Trinity, and Jin head to the Cauldron to leave the Embryo. They encounter Hazama torturing Rachel. Naoto shows up. He allows them to rescue Rachel and stops Hazama from making Ragna turn into the Black Beast. Hazama jumps into the Cauldron. Naoto returns to his world. Rachel brings Ragna, Jin, and Trinity to the Gate. Ragna hugs Rachel goodbye.
Ragna, Jin, and Trinity find Terumi at the Gate. He's consumed Noel to prevent Interventions against him. He intends to destroy all the worlds the Master Unit creates until she creates a world of pure fear for him. His goal really seems rooted in outdoing the Master Unit and having complete freedom. Jin fights Terumi and manages to "perceive" him. Ragna makes himself go out of control and activates BlazBlue. Ragna fights Terumi and manages to pull Terumi out of Susano'o. Trinity helps Jin take the Susano'o Unit while the Master Unit watches, then Jin slays Terumi and Ragna. By allowing Jin to take control of Susano'o to slay them under the Master Unit, Susano'o is now a hero who saved the world from the Black Beast and therefore nobody is afraid of Terumi.
Ragna and Terumi are suddenly past the Gate in Azure Horizon. Terumi says they're here because the Azure responds to those who desire it. One of them will take it and one of them will die for good. They fight and Ragna kills Terumi. Ragna retrieves Noel.
Noel and Ragna go to The Origin. Noel consumes The Origin. Ragna says that he's The Origin's dream. In order to allow the world to move forward, he must cease to exist. Trinity returns Jin to a Jin body so that he can't stop Ragna. Jin tries to stop Ragna anyway and fails. Ragna tells them he wants to protect their world and they have a sibling hug.
Ragna entrusts the Susano'o Unit to Trinity, who puts it deep in the Boundary. She says that the Susano'o Unit was the catalyst for this mess and humans should have never found it.
Ragna goes to the Master Unit and talks to a soul inside named Saya. He apologizes for making her wait so long and says they'll be together from now on. He activates the Master Unit. Amane appears to say goodbye to Ragna. Ragna has the dreams of all the Chosen with him and will use them to create a world that won't be affected by Intervention from Amaterasu or Takamagahara. A new world is created.
Noel, Lambda, and Nu now reside at Celica's church. Bang leads a reconstruction of Ibukido. Everyone else also pursues their dreams.
Tsubaki finds Rachel on top of a hill and says she's come to fulfill their promise.
AD 2200/XX: Irrelevant Side Plots
Mai and Hibiki don't do anything noteworthy.
Bullet finally finds out Tager was her captain. She can move on with her life now.
Bang, Litchi, and Tao encounter Arakune. Arakune is much more powerful due to the Seithr he absorbed in Chrono Phantasma. Litchi gets swallowed by Arakune and finally finds Roy in the Boundary. Roy tells her that he loves being in the Boundary because he has access to so much information. Roy asks her to destroy his vessel (Arakune) so he can stay in the Boundary forever. Litchi is spit back out. Bang doesn't want Litchi to have to kill Arakune, so he knocks her out and fights Arakune himself. This plotline gets interrupted when everyone starts turning into Seithr and isn't revisited.
Carl tries to discover the secrets of the world. He learns a lot from Relius and explores the Cauldrons on his own. He sees the structure of the world, but disagrees with Relius about the importance of unstable souls. Something happens to his left eye and he starts wearing a Relius mask.
Relius wanders around doing research. He wants to create a new world with Ignis as the new Master Unit. After Izanami is killed and Terumi takes Susano'o, Relius goes into the Boundary for "verification," whatever that means.