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The Christian Era
- The Heavenly Gods launch the first Vertex attack on humanity, resulting in massive casualties and large-scale destruction.
- Several young girls across Japan find sacred weapons that imbue them with divine power to repel the Vertex. Other girls begin receiving oracles and prophecies. Several of these girls make their way to Shikoku Island, revealed to be a safe place. These include Wakaba Nogi, Hinata Uesato, Tamako Doi, Anzu Iyojima, Yuna Takashima, and Chikage Doori.
- Other girls remain in their own cities to defend them, including Utano Shiratori and Mito Fujimori of Suwa, Natsume Kohagura of Okinawa and Sekka Akihara of Hokkaido.
- The Shinju, a conglomeration of land gods in the shape of a tree, manifests in Shikoku and creates a barrier which repels the Vertex from the island.
- The Taisha (Grand Shrine), an organization dedicated to worship of the Shinju, forms a theocracy in Shikoku.
- The Taisha gather girls who have received divine power and classifies them as Heroes. Meanwhile, girls who have been granted oracles are classified as Miko and are cloistered within Taisha headquarters.
- Wakaba, Tamako, Anzu, Chikage and Yuna are gathered together at Marugame Castle to receive education and training as Heroes. Hinata, who as a Miko has the strongest connection with the Shinju, is allowed to study with them.
- Natsume guides a group of evacuees, including the Akamine family, from Okinawa to Shikoku and disappears. Okinawa falls to the Vertex.
- Sekka disappears and Hokkaido falls to the Vertex.
- The Taisha develop a transformation ap[ which allows Heroes to directly access the Shinju's power through their smartphones.
- The Taisha develop a "Trump Card" system that allows Heroes to channel certain land spirits and youkai, classified as fairies, in battle, at the cost of their physical and mental health.
- The first cases of Uranophobia Syndrome begin to appear in people who witnessed the Vertex attacks.
- Shiratori and Mito die in battle, and Suwa falls to the Vertex, leaving Shikoku as the last bastion of humanity.
- The Hero Team of Shikoku begin their first battles defending Shikoku and the Shinju from the Vertex.
- A fused Vertex, Sagittarius-class, appears for the first time.
- Tamako tries to offer a Gemini-class Vertex udon as a peace offering, but to no avail.
- Yuna is injured in a battle protecting Wakaba from an attack.
- Anzu shows Wakaba how their actions have benefited and inspired the people of Shikoku, leading to Wakaba changing her motivation from revenge to protecting the people.
- Hinata receives an oracle of a massive Vertex attack in the near future.
- The Battle of Marugame Castle is fought, which ends with the Heroes victorious thanks to Anzu's tactics.
- The Heroes, together with Hinata, go on an expedition to Suwa to look for survivors, passing through the ruins of Osaka and other cities. They find some of Shiratori's possessions, but return having found no survivors.
- The Taisha begin to censor information, hiding the lack of any survivors outside of Shikoku and banning certain books.
- The first "complete" Vertex, a Scorpio-class, materializes. Anzu and Tamako are killed in the ensuing battle.
- The deaths of two Heroes begin to cause unrest in the people and public opinion of them begins to decline rapidly, as does Chikage's mental health due to the effects of her Trump Card.
- The Leo Vertex, much larger than any Vertex before it, appears outside of Shikoku. Yuna attempts to summon Shuten-Douji once again but is unable to and is critically injured in the process. The Heroes retreat.
- Chikage's rapidly deteriorating mental state causes her to attack civilians before being detained by Wakaba.
- Chikage attempts to murder Wakaba during a battle before being stripped of her divine power by the Shinju. She later dies defending Wakaba from an attack.
- Chikage is buried without honors and her name is stripped from all public records.
- Yuna receives fatal injuries during a climactic battle, but before death her spirit is absorbed by the Shinju as an arahitogami, or human god. Wakaba survives, albeit with heavy injuries.
- The Leo Vertex overwrites the world with a sea of fire. The Shinju creates a conceptual barrier to protect Shikoku Island and hiding the outside world from the people.
- The Taisha call for an armistice through the Festival of the Fire Offering, a sacrifice of six Miko to the sea of flames. Hinata uses her influence to avoid becoming a sacrifice.
- The Taisha change the characters of their name from "Great Shrine" to "Amnesty" to show their subservience.
- Hinata becomes the new head of the Taisha, and together with Wakaba spearheads reforms and secret research with the goal of humanity defeating the Vertex in the future.
- The Christian Era ends, and 2019 AD becomes Year 1 of the Divine Era.
The Divine Era
Between DE 1-297
- The Taisha begin a new practice of naming any girl who performs a reverse clap at birth Yuna, in reverence to Yuna Takashima.
- The Trump Card system is removed from the transformation app.
- Cults worshiping the Vertex and the Heavenly Gods begin to appear in Shikoku. Members of the Akamine and Miroku families are given divine power to combat the cults.
- The cults are defeated by Yuna Akamine and Renge Miroku. However, the Miroku family is disgraced due to Renge's hesitation and falls into obscurity, while the Akamine enjoy prominence as the Taisha's enforcers.
- The last person born in the Christian Era dies.
- The Taisha censor all mentions of the Vertex, the Heavenly Gods, the Christian Era and the outside world, telling people that humanity had been wiped out by a virus.
- Anticipating that the ceasefire would soon end, the Taisha perform a search for new Heroes. The ones selected are three sixth-graders from Kagawa Prefecture: Mimori Togo, Sonoko Nogi and Gin Minowa.
- Mimori is adopted into the powerful Washio family and given the name Sumi Washio.
- The three Heroes fight their first battles while being mentored by Aki-sensei, a Taisha worker and their homeroom teacher.
- Gin is killed in battle, having driven out the Scorpio, Saggitarius and Cancer Vertexes alone. Gin's terminal is recovered.
- The Virgo Vertex attacks during Gin's funeral but is defeated by the two enraged Heroes.
- The Taisha begin to research a way to further protect the two remaining Heroes, using Anzu Iyojima's research on the Trump Cards as a base.
- The Taisha create the Hero System, which manifests a fairy to protect a Hero from all harm and maintain their link to the Shinju and grants the Heroes greater power than before.
- One functionality of the Hero System is Mankai, which allows a Hero to temporarily channel great power from the Shinju itself, but which will require a sacrifice of a random bodily function, called the Sange.
- The Heroes are informed of the Mankai functionality but are not told of the Sange. The Heroes' families are given lavish compensations and gain greater status in the Taisha for their compliance.
- In a battle against several Vertex including Leo, Sumi activates Mankai twice and loses the use of her legs as well as her memories of the past several months, thus becoming incapacitated.
- Sonoko accidentally ventures beyond the Shinju's barrier and witnesses the sea of fire outside, where the Vertex infinitely regenerate and multiply. Sonoko, now fighting alone against twelve Vertex, activates Mankai a total of twenty times and emerges victorious, albeit at the cost of almost all bodily function.
- The Great Seto Bridge is destroyed due to the damage to the Jukai, resulting in the deaths of two Taisha workers named Inubozaki who were evacuating civilians.
- The Taisha begin once more to search for Heroes, expanding their search to across the entirety of Shikoku.
- Sumi, now wheelchair-bound and missing her memories of her tenure as a Hero, is given back to her birth mother and retakes her birth name of Mimori Togo.
- The Togo family is given a large house in as compensation next to the Yuki family, whose daughter, Yuna Yuki, scored higher on the Hero Aptitude Test than anyone else tested. The Taisha, knowing that Yuna is bound to be selected as a Hero, hope that she and Mimori will be able to work well together.
- Sonoko is enshrined in a Taisha hospital, where she is revered as a demigod close to the Shinju and is given anything she desires, except being able to see Sumi again.
- Aki-sensei is promoted to a Taisha priestess.
Between DE 297-300
- Three new girls, middle-schoolers who attend Sanshu Middle School in Kagawa Prefecture, are selected to become Heroes by the Shinju: Yuna Yuki, Fu Inubozaki and Itsuki Inubozaki.
- Fu Inubozaki, daughter of the two Taisha workers killed in 297, is instructed by the Taisha to form a "Hero Club" with Yuna and Mimori, along with her little sister Itsuki once she begins to attend middle school, and to hide its purpose from them.
- The Hero Club helps out other clubs and performs community service around town, with all but Fu oblivious to its true purpose as a way for the future Heroes to grow as a team.
- The Taisha gathers several other girls who have Hero aptitude but were not chosen in order to find a candidate worthy of inheriting Gin Minowa's Hero terminal. These girls include Karin Miyoshi, Mebuki Kusunoki and Yumiko Miroku.
- The Virgo Vertex attacks, causing the Hero Club to be thrust into battle. Fu, Itsuki and Yuna manage to transform, but Togo's repressed traumas from her previous tenure prevent her from transforming. Virgo is defeated by Yuna.
- The Sagittarius, Scorpio and Cancer Vertexes attack. Togo manages to transform to protect Yuna and defeats the three Vertex, unknowingly getting vengeance for her fallen friend. The other girls note how Togo has three fairies compared to their one each and seems oddly experienced.
- Karin Miyoshi is selected to inherit Gin's terminal. She is sent to live in a Taisha-furnished apartment in Sanshu.
- The Capricorn Vertex attacks, but the Hero Club's battle is interrupted by Karin, who swiftly defeats Capricorn alone. She introduces herself to the Hero Club and transfers to their school to supervise them under orders from the Taisha.
- Itsuki submits an audition to an idol agency.
- Sonoko Nogi, using one of her twenty-one fairies, draws the other Heroes into a dream world in order to simulate what may happen if the Shinju's barrier were to be breached before pitting them against her memory of the Leo Vertex. Satisfied with the Hero Club's resolve, she sends them back to the real world without their memories of the incident, promising to meet them again. After this, the Taisha revoke Sonoko's terminal.
- Seven Vertex attack: Aries, Pisces, Aquarius, Libra, Taurus, Leo and Gemini. In the ensuing battle Yuna, Togo, Fu and Itsuki all activate their Mankai and emerge victorious. Having defeated all 12 Vertexes, the Heroes believe their battles to be done.
- The Heroes who activated Mankai begin to suffer Sange: Yuna loses her sense of taste, Mimori loses hearing in one of her ears, Fu becomes blind in one eye and Itsuki becomes mute. Togo begins to monitor everyone's condition despite the Taisha's assurance that these are temporary side-effects that will go away soon.
- The Heroes begin to receive compensations. They also receive word that despite having defeated all of the Vertex, another attack is imminent.
- A second Gemini Vertex attacks. Yuna, Fu, Itsuki and Togo have received new fairies, but Yuna's use of her new fairy's power leaves the other Heroes apprehensive since their bodily functions have not been restored yet.
- After the battle, instead of being returned to their school rooftop with the others, Yuna and Togo find themselves summoned by Sonoko to the roof of her hospital. There, she reveals the truth about Mankai and Sange to them, as well as her past as a former Hero who underwent twenty Sange.
- Togo begins to test the fairies powers by attempting to commit suicide several times in various ways. She later reveals to Yuna and Fu that the fairies have made them effectively immortal, and relays the truth about Sange to Fu.
- Togo visits Sonoko once more, who reveals the truth of the outside world to her. Togo, in despair that her friends were doomed to eternal suffering, begins to destroy the Shinju's barrier in hopes of destroying the world.
- Fu learns about Itsuki's idol audition. Realizing that her sister's dreams had been destroyed, she attempts to exact vengeance on the Taisha only to be stopped by Karin, Yuna and Itsuki.
- The Taisha, alarmed at Fu's and Togo's actions, ask Sonoko to transform once more and defeat them. Sonoko refuses, wishing to see what the Hero Club would do now that they had the truth.
- Yuna, Karin, Fu and Itsuki meet Togo in the outside world to stop her, where Togo tells them the truth of the outside world and manages to escape them. Karin and Yuna are split up from the Inubozaki sisters.
- Karin, protecting a despondent Yuna, defeats five Vertex on her own, activating Mankai five times despite knowing the cost, and loses her sight, her hearing and agency in the right side of her body. Karin encourages Yuna to save Togo.
- Fu and Itsuki confront Togo, who is guiding the Leo Vertex to the Shinju. Togo incapacitates the two of them with her Mankai, but the Leo's shot at the Shinju is stopped by Yuna, who proceeds to defeat Togo and change her mind. However, the Leo Vertex, left to gather energy during the duel, is left free to make a charge at the Shinju. Meanwhile, Yuna's Mankai wears off and Yuna loses the use of her legs.
- Fu, Itsuki, Togo and Karin combine their Mankai to stop Leo's charge, while Yuna, forcing herself into a Mankai while untransformed, defeats it once and for all. However, this comes at the price of Yuna's entire body, and her soul is brought into Takamagahara, the realm of the Heavenly Gods.
- The Shinju, in gratitude to the Heroes' heroism, begins to replace the girls' sacrificed functions with divine constructs. However, Yuna's spirit remains trapped in Takamagahara until Wakaba's spirit, in the form of a crow, guides her out. Yuna's entire body was replaced with a divine construct, making her a Misugata, an extremely sacred being.