The episode opens with Rin being chased to the rooftop by a female assassin named Laura. Severely wounded, Rin falls down to her death. In the next scene, she wakes up unscathed in her apartment and returns to work, looking for a stray cat she was hired to find. Circumstances lead her to run into a man named Kōki Maeno in a quiet street. After knocking out several agents pursuing Kōki, Rin takes him to her office where he tells her and her partner Mimi that although he is not amnesiac, he feels that his memory is fake and he would like to know why he is pursued. Through Rin's links, they find out that Kōki is connected to the Aoyama Pharmaceutical company. With Mimi's help, they infiltrate its labs but are captured. Rin is tortured to death by the sadistic chief researcher Sayara Yamanobe, while Kōki is revealed to be a runaway cloning test subject. Miraculously, Rin survives, completely healed of her injuries, and confronts Yamanobe, leaving her in the hands of other delirious test subjects. As the compromised facility is demolished by Aoyama Pharmaceutical, Rin escapes with Kōki and hands him a gun, for him to decide what he wants to do with his life. After he seemingly commits suicide, Rin leaves the scene. The next day he appears in her office, wounded on the head and with the missing cat in his hands, and asks to become her business partner.

One year after the Aoyama Pharmaceutical incident, Rin is hired to track down a rare postage stamp and visits an old homeless man she calls "Sensei" to gather information on it. He is revealed to possess one himself but it is stolen soon afterwards and he is severely injured. As Rin looks through his belongings, she is attacked by Laura who quickly detonates a suicide bomb. Meanwhile, Maeno meets a girl named Yuki who is looking for an "angel" that may know the whereabouts of her missing brother Shōgo. Attracted by the explosion, he finds Rin's mutilated body and is visibly shaken by witnessing her regenerate. Later, Mimi explains to him that both Rin and herself are immortal because of the "time spores" inside their bodies. In the meantime, several people including Rin's client are murdered and before long, she confirms that Yuki's brother turned into an "angel" due to contact with time spores leading him to commit the recent murders as acts of revenge. She also reveals that angels are natural enemies of the immortals like herself: in their presence, immortals are overcome with lust and angels use that time to devour them. Rin then deduces who Shōgo's final victim would be and confronts him only to seemingly give in to sexual desire. As the angel starts feasting on her, she manages to kill him. An apparition of Eipos, a demigod appearing briefly throughout the series, emerges nearby to claim Shōgo's time spore but Rin gives it to Maeno instead and he, in turn, to Yuki. In the final scene, Rin returns the stolen stamp to "Sensei" who laments how his life was wasted on it.

Twenty years after the events of episode two, Maeno is still working for Rin and is now married to Yuki and has a son with her. The episode opens with them receiveing a call from a girl wanting to meet Rin. However, she only says one cryptic sentence and dies in front of her, which reminds Rin of a story she heard from a friend back in 1945. She soon discovers that the girl displayed the same symptoms as subjects of a biological weapon "Higan" test on the so-called "Death Island". The Island has been officially demolished and Tamotsu, a police officer and Rin's friend, confirms that its former residents were among the victims of each recent bombing in Tokyo. Soon after that, Rin is captured and brought to the Death Island. Mimi decides to visit Rin's unnamed informant from episode two who demands lesbian sex with her in return for information on Rin's whereabouts. She informs them that the group behind the bombings and Rin's capture is called "Kudoru" (Sanskrit: Evil). Meanwhile on the Island, Rin discovers that Sayara Yamanobe survived as an immortal but has to rely on a powered exoskeleton to move. After being dissected, Rin escapes but is chased and killed again. Sayara explains her plan to exterminate humans with Higan, leaving only immortals on Earth. Maeno arrives on a helicopter to free Rin but is fatally shot. With his last strength, he consumes Shōgo's time spore and turns into an angel. After carrying Rin to safety, he returns to devour Sayara but Eipos arrives to remove both their time spores, killing them instantly. The next day, Rin and Mimi stay in their office, visibly shaken by Maeno's death.

The episode opens with Maeno's son Teruki having sex with a girl named Ruon via a virtual reality network called "2.0". He offers to meet her in real life ("1.0") but she refuses. Later, he meets Ruon in 1.0 only to witness her murder. Teruki finds Tamotsu, who brings him to Asoogi Consulting. Mimi explains that Ruon is actually an AI created by Katsuyuki Kamiyama, modern von Neumann. Rin takes Teruki for a walk but they are attacked by Laura, now a cyborg, who mutilates Rin considerably. Teruki is shaken by the sight of Rin regenerating so she tells him about time spores and immortals. Teruki suffers a mental breakdown but she comforts him. Mimi and Tamotsu discover that Ruon was created during "Project L'Isle-Adam", based on Kamiyama's daughter whom he killed. Ruon calls to invite Teruki to 2.0 but they are attacked by Kamiyama and Mimi severs the connection. Immediately thereafter, commandos attack the office forcing them to flee. En route, Mimi explains that Ruon might have been an attempt to create "The Future Eve". The military attacks again and Teruki is taken away. Back in the office, Rin and Mimi realize that the girl Teruki met in 1.0 was an android with Ruon's AI. Tamotsu calls to tell the flight number that Teruki is on but is fatally shot by a sniper. Rin boards the plane, only to find Kamiyama shot by android Ruon. Ruon is revealed to have manipulated the military to get Teruki, the only person she cares about. Rin pushes Teruki out of the plane with a parachute and after a brief fight, she and Ruon fall out of the plane and into its jet engine together. Some time later, Teruki finds that Rin's office was demolished. Mimi is shown bringing flowers to where Tamotsu was shot. Rin's fate is uncertain.

Thirty years after episode four, the borders between 1.0 and 2.0 have been erased completely and it is now possible to "download" things into the real world. Rin took 25 years to regenerate her body and suffered retrograde amnesia in process. Teruki became a successful businessman and Mimi, a Buddhist nun. Meanwhile, Eipos disguised Laura as Rin and made her hunt immortals for their time spores. The episode begins with Teruki's daughter Mishio discovering his records of Rin and by chance, meeting her amnesiac self. Rin is working for James & Will company, whose CEO is an immortal and is soon killed by Laura. Mishio finds her body, and thinking that Rin killed her, starts following her around. She witnesses a man named Ihiko propose to Rin, which she refuses, telling him of her amnesia. After Mishio asks Teruki about Rin, he finds her but decides that it's better for her painful memories not to return and doesn't contact her. He then finds Mimi who tells him that Rin is apparently hunting immortals. Meanwhile, Rin accepts Ihiko's new proposal and the two make love, when Laura attacks and kills them both. This returns Rin's memories and she escapes with Mishio to Teruki's estate. After a conversation with him, Rin and Mishio take a train to Kyoto, where Mimi's temple is located. Meanwhile, Mimi invites three other immortals, anticipating Laura's attack, but Laura brings angels with her who proceed to devour them. Rin arrives and defeats Laura and the angels, only to witness Mimi raped by Eipos. Eipos is then revealed to be an hermaphrodite god and removes Rin's time spore, presumably killing her.

Shortly after the end of episode five, Rin wakes up in Eipos' castle at the foot of Yggdrasil, the mythical tree that generates time spores, since Eipos let her regenerate instead of consuming her spore. She is then locked in a room with a masked angel and kills him, only to discover that it was Ihika. Meanwhile, Mimi and Mishio desperately search for Rin and learn the location of Eipos' castle from the informant. Tajimamori, former Guardian of Yggdrasil, invites them to his castle, explains that his son Eipos aims to become the new eternal Guardian, and opens a portal to Eipos' castle for them. There, Rin is losing the battle against Laura but Eipos double-crosses her and Rin escapes. In retaliation, Laura teams up with Mimi and Mishio and leads them to Yggdrasil. Rin is already there and meets Tajimamori, her millenia-old love. They have sex until Eipos arrives, kills his father, and pushes Rin into Yggdrasil. Mishio tries pulling Rin out and fails but Rin manages to grab Kōki's time spore (that Rin found in the sea after episode four and Mishio unwittingly brought to the castle) from her necklace. As Yggdrasil tries to merge with her, Rin consumes Kōki's spore and his spirit helps her to break free. Mishio, revealed to be Tajimamori's descendant like all Maenos, pulls Rin out and back to the castle. Eipos attacks them but Rin, now the new Guardian of Yggdrasil, pushes Eipos into it himself. Before he is consumed, she feeds Tajimamori and Laura's spores to him. In the epilogue, Rin gives birth to Tajimamori's son and continues living in Eipos' castle with Mimi and Mishio. Her closing narration reveals that their son is linked to the Yggdrasil and this link will spread throughout mankind with his descendants.