Akari Taiyo is a girl who takes after her late mother Hinata as an apprentice fortuneteller. She lives with her aunt and uncle, and her cousin Fuyuna Shinzaki, who is jealous of the attention Akari receives. One night, Akari has an apparent dream in which she is attacked by a giant plant monster, and sees herself as a magical girl killing it. When she awakens, she finds Fuyuna lying dead in her bedroom. The events of the previous day then repeat themselves; this time Fuyuna is completely absent, and Akari and her relatives appear to have no memory of her. Akari later goes to the fortune-telling house where she works to find it has been set ablaze by a middle-aged man, who transforms into a giant, flaming monster and attacks her. Akari transforms into a magical girl wielding the power of the Sun Tarot and fights back, but is overpowered and knocked unconscious. She is rescued by three other magical girls, who kill the monster and bring her out of the burning house.

Akari awakens at the Sephiro Fiore institution, where the headmaster Etia Visconti tells her about the organization's use of the Elemental Tarot in their ongoing battle against the Daemonia, monsters that possess humans overtaken by negative emotions. Akari moves to the school and meets her new teammates: Seira Hoshikawa, who wields the Star card; Luna Tsukuyomi, who wields the Moon card; and Ginka Shirokane, who wields the Temperance card. During a seemingly normal day of lessons, the girls are dispatched to kill a Daemonia. As Akari fights the monster, she regains her memories of Fuyuna and loses her transformation out of shock, forcing Luna to help her retreat whilst Seira and Ginka finish their duty. Etia explains to Akari that those possessed by Daemonia cannot be saved, and that everything pertaining to that person's existence is erased once they are killed. Filled with anger and guilt, Akari runs from the academy and cries in apology to her aunt, who still remembers nothing of Funuya. Later, Akari spots a possessed man attempting to kill a happy father and son, and becomes conflicted on whether to act or not.

Akari chooses to fight against the Daemonia to protect the innocent, but once again hesitates to finish it off. Priscilla Twilight and Meltina Melvis, wielders of the Fool and Magician cards, arrive to fight it. Akari hears the Daemonia's voice crying for help and stands against Priscilla and Meltina. The Daemonia escapes, and Akari is brought back to Sephiro Fiore and detained in a cell for her disobedience. The next day, Akari tells Etia and deputy head Ariel Valtiel Wescott about the voices she heard. The two hesitate to believe her, but let her out when she promises to fight again. Akari and her companions prevent the Daemonia from killing a kindergarten teacher and her students. Akari attempts to listen to the voice, which tells her that it no longer wants to kill and asks Akari to kill it, to which Akari reluctantly obliges. Akari accepts her destiny, though choosing to respect the wishes of those who are possessed, to Etia's approval.

A young painter named Kiyone feels resentment towards a popular painter, Yume Hashiyagama. One night, Kiyone comes across a mysterious silver-haired fortuneteller named Cerebrum, who gives her a tarot card and tells her to be true to her feelings. The next day, when she sees Yume kissing the boy she has a crush on, she uses the power of the tarot card, which is revealed to be a Diabolis Tarot card that creates Daemonia, in order to have Yume killed by a truck and take her fame at the art contest with a twisted piece of her own. Meanwhile, Akari becomes upset at Seira, who claims only weak people become possessed by Daemonia, lamenting that she was unable to help Fuyuna when she needed it. Driven further by the Daemonia's influence, Kiyone begins killing more of the people who had looked down on her, at which point Akari and the others are called to face her. As they fight, Luna also becomes able to hear the Daemonia's resentful thoughts by touching Akari, with Seira killing it off before Akari can hear her true feelings. Afterwards, as Akari reads a journal left behind by Fuyuna, Luna states she is grateful to be able to hear the Daemonia.

Ginka's father Yataro, who helps fund Sephiro Fiore's operations as thanks for helping his family out when they were in debt, comes to visit and invites the girls to a fancy party. Whilst there, Ginka and Yatarou hear about one of his old friends, Honda, who is facing financial struggles and is now in debt to loan sharks. That night, as Honda prepares to commit suicide, Cerebrum, this time taking the form of a young girl, gives Honda a Diabolos Tarot card that he uses to kill the loan sharks and escape his debt. The next evening, the silver-haired person instructs Honda to kill Yataro for possessing the Elemental Tarot user's blood, sending a wave of environmental hazards to attack him, but Akari and the others arrive to help him. Learning that the Daemonia is Honda, Ginka uses Akari's link to hear his thoughts, lamenting his weak heart. Realizing the only thing she can do for him is let him rest in peace, Ginka destroys the Daemonia. Being the only one left who remembers Honda, Ginka sympathizes with Akari's concerns.

Seira helps Priscilla and Meltina fight a pair of Daemonia, commending their teamwork while stating she has never considered her own group a team. Later, a pair of schoolgirls, Minori and Hanae, encounter Seira and Ginka and befriend them. After Minori ends up misplacing her phone in Seira's bag, they meet with her again, during which time Minori undergoes an attack caused by her heart problems. As Minori is hospitalized, Seira recalls how her old friend, Manami, was killed by a Daemonia. Meanwhile, Hanae is lured by the power of the Diabolos Tarot card, using it to kill a compatible donor to allow Minori to have an operation. Back at Sephiro Fiore, Seira requests to join Priscilla's team, but Levi convinces her to give Akari's team one more chance. When she discovers Hanae has become a Daemonia, she agrees to use Akari's strength to listen to Hanae's voice, asking her to take care of Minori in her place. Seira hesitates to finish her off, but Akari convinces her that because they hear the Daemonia's voices, they must strengthen their resolve, allowing her to make the kill. With a hairpin Hanae bought with Seira the only thing left behind of her new friend, Seira gives it to Minori, who is able to undergo her surgery. Afterwards, Akari tells Seira about how she feels hearing the Daemonia's voice is important, while Seira confesses all of her insecurities to her.

Etia and Ariel are informed that the wielder of the Lovers card in Sephiro Fiore's Moscow branch has disappeared. Etia decides to give the girls a day off, not wanting to concern them with this development so quickly. As the girls tour the city, Akari and Seira become more friendly with each other, though Luna appears concerned. The girls meet Akari's old fortunetelling mentors Mama Nagasaki, Lymro, and Hanayume, who let them spend the night at their new home. Mama Nagasaki reads the girls' fortune, and predicts that their future will be filled with hardship and destruction. The girls affirm that they will be able to overcome any challenges ahead as long as they are together. They return to the academy where Etia and Ariel are waiting for them, prepared to tell them of their next assignment.

Etia reveals her findings concerning the Lovers user's disappearance to the girls, theorizing that if a Daemonia carrying a card that matches that of a tarot user is defeated, that user will disappear along with them. She begs the girls to flee should they encounter their counterpart. As the girls have conflicting opinions about what the right thing to do is, Luna, who desires to protect Akari at any cost, feels agitated when she seems to take Seira's side. Later, as the girls fight against another Daemonia, they come face to face with Temperance's counterpart card, which deals whatever damage it takes to Ginka, forcing them to retreat. Given some time off from action, Ginka visits Yataro, who assures her that she helps bring balance to her group. Ginka decides to face her counterpart alone, with the others helpless to do anything but watch as they defeat each other, vanishing into nothingness.

As everyone in Sephiro Fiore becomes saddened and frightened by Ginka's disappearance, Luna is called by her butler to stay at her villa to rest. Whilst there, she recalls how her twin sister, Serena, disappeared one day, as well as remembering when she first awakened to her powers. As Luna contemplates her feelings for Akari, she is seemingly visited by her, making her feel a lot better. However, when Luna expresses her feelings to her, it is soon revealed that the Akari she has been speaking with is actually Cerebrum, who forces a Diabolis card into her body, transforming her into a hybrid of a Daemonia and an Elemental Tarot user.

Luna, in her mutated form, appears before Akari and Seira, biting Seira in the neck, leaving her with a butterfly mark. After retreating back to Sephiro Fiore with Seira in tow, Akari helps Priscilla and Meltina escape from a battle against their counterparts. Akari is informed about Cerebrum from Laplace and Shrodinger, the messengers of the Leguzario organization that formed Sephiro Fiore, informing her that she will inevitably have to fight Luna. Akari asks Seira for her help, only to learn that the bite she took from Luna had sealed off her Tarot powers, leaving Akari the only one capable of fighting against the Daemonia. After fighting Daemonia for several days straight, Akari eventually comes up against Luna, barely managing to escape after Luna's human will holds herself back. Whilst visiting her mother's grave afterwards, Akari encounters a small girl who had allegedly lost her mother, barely avoiding running into another trap laid out by Cerebrum. As Seira hears rumors about a wolf in the mountains, Cerebrum uses his contacts to incite a mob to attack Sephiro Fiore, forcing Akari and the others to retreat.

Akari and the others take shelter at Nagasaki's mansion, where Nagasaki tells Etia about her time with Hinata and Akari. Meanwhile Seira searches an old abandoned building and finds Luna with Cerebrum, who tells Seira that Luna had wanted her to disappear of her own free will out of jealousy over Akari. Cerebrum tells Seira that she'll be able to get back her powers if she kills Luna, giving her only a few hours before Luna wakes up. The next morning, Etia makes the decision to defy Leguzario and tell Akari the secret being hidden from her, that her father was someone infected by the Daemonia, with Akari herself being half Daemonia. After learning this, Akari goes to confront Cerebrum, who offers to save Luna and Seira in exchange for her coming with him, whilst Seira is forced to defend herself from the now awake Luna.

Wanting to save Seira and Luna, Akari agrees to Cerebrum's conditions and is transported to a place called the Sephirothic Tree, where he intends to use a device called the Clessidra so that they can mate, returning Seira and Luna to normal in exchange. Inside the Clessidra, Cerebrum forces Akari to relive the day Fuyuna died,hearing her thoughts of hatred towards her over and over, until she loses enough of herself to be his. Arriving at the Sephirothic Tree, Seira and Luna face up against an army of tree Daemonia, which they manage to defeat thanks to the mysterious arrival of Ginka. Meanwhile, Akari, believing that Fuyuna became a Daemonia because of her, is hanging on to the last of her sanity.

Etia and Ariel are given a key by Leguzario that will let them free Akari from the Clessidra, but only with the right timing. Meanwhile, it is revealed that Ginka was able to defeat her counterpart and break free from the dimension she was trapped in thanks to Akari. Back in the Clessidra, Akari is finally able to hear Fuyana's true thoughts, that she truly loved her but was overcome by her jealousy. Stating that she loves her too and accepting her destiny, Akari manages to overcome the darkness. As Cerebrum attempts to kill Akari, Etia and Ariel use the key to unlock their previously sealed powers, allowing them to break Akari free. After failing to lure Akari and the others into darkness again, Cerebrum transforms into his ultimate form, but all the tarot users unite against him, allowing Akari to break through and destroy him. Afterwards, as the girls head to an overseas Sefiro Fiore branch, Akari finds a note left behind by Fuyuna, encouraging her in her path to one day save everyone from the Daemonia.