The story begins on October 3rd where Koishi thinks about fishing, and nearly killed two people at Koumakan for a fishing rod. Satori is alerted to stop her, dragging Koishi home and locking her up, then Satori returns to apologize the next day. Remilia lets her go, but Satori warns that Koakuma isn't innocent as she seems, which agitates them. Satori gets a clean shot at Koakuma, but Remilia decks her before she could move.

Concurrently, Koishi escapes her room and Gensōkyō descends into madness by 4:25pm on October 4th, so Yukari and Reimu begin their investigation into Chireiden and Koumakan respectively. With the montage of bloodshed and falsified memories, Satori begins to head home. During this, Yukari mistook Koishi as the threat in Chireiden, neutralizes her, then Reisen²⁾ reveals herself and executes Yukari.

Koishi proceeds to borrow Yukari's body, though Yukari urges her to check in on Reimu at Koumakan. As for Reimu, she identifies Koakuma as the threat, and Udonge shows up to stop Reisen's ambush. Returning to Chireiden, we see Satori watch the souls being redirected there, but the Watatsuki Sisters decide to neutralize her for being a risk to their 'Moonlight Descent Ceremony' (月影降臨術, Tsukikage Kōrin-jutsu) plan.

At this point, we are shown how the Satori got their bodies, Koishi's trauma, and how the invading Lunarians coerced the Satori into their 'absolute world peace' plan by turning all living beings into third eyes. We also learn that the Lunarians tried to abolish the outside world's sorrows by creating a madness-inflicting moonlight, which solely impacts Gensōkyō, and Eirin's rushed 'rain of detoxification' solution.

The final part opens up with the Lunarians warning the outside world of an 'imminent alien threat' before this story even began. Koakuma boards the 'Vishoka'³⁾ ship with Patchouli, then our protagonists head to the Hakurei Shrine, finding Toyohime making sure that their Great Hakurei Barrier will shatter by eliminating them. After their loss, Kaguya curiously hands 'Koishi Yakumo' a detoxification vial and a bit of advice.

As foretold, the Great Hakurei Barrier shatters at 6:59pm on October 4th, so the Lunarians readily send their 'Vishoka' ships out to eradicate all of Gensōkyō's former inhabitants, now turned into kaiju, while Koakuma harnesses all of their powers. Toyohime taunts Satori for raising Koishi despite, having no relation to her, then Yorihime is killed as she eliminates the last three kaiju.

With the 'perfect conditions' achieved, the Lunarians blast the moon's eye open, turning all living beings into third eyes. Seven years have passed. We find Koishi and Yukari, separated, but living together in a south German residence. Yukari grieves with survivor's guilt, then attacks Koishi's escapism, claiming that she closed her eye for selfish, manipulative reasons, so Koishi pokes her third eye open to 'face reality' with her.

The story tells us the myth of Tsukiyomi being separated from her lover and becoming the moon,⁹⁾ then fast forwards to the Common Era where Eirin would voluntarily become pregnant with Kaguya's clone during The Tale of the Bamboo Cutter before Kaguya had to return.¹⁰⁾ We haven't found out what happened to her clone, technically speaking, but most suspect that it had something to do with Koishi.

Gensōkyō is founded in the late 19th century, then Sanae's backstory likely occurs in the mid 20th century.¹¹⁾ Eventually, the Lunarians embark on the 380,000km trip to invade Earth in 1972,¹²⁾ slowing once they're 400km away¹³⁾ in 1982, and incidentally shred Koishi's body.¹⁴⁾ From here, tragedy falls upon the two Satoris, roped into their plans in the early 1980s,¹⁵⁾ then Koishi rampages.¹⁶⁾

Forty years have passed since the Lunarians brought world peace, reeducating humanity,¹⁷⁾¹⁸⁾ and our long three-day story finally begins here. The Lunarians warn humanity of an 'imminent threat' as Koakuma and Reisen begin experimenting.¹⁹⁾²⁰⁾ In the following day, Satori apologizes at 4:00pm,²¹⁾ the 'madness' starts to soak Gensōkyō at 4:25pm, and Flandre shatters the Great Hakurei Barrier by 6:59pm.²²⁾

After the Lunarians systematically kill off Gensōkyō's inhabitants in their Kaiju form, being hailed as saviors, they conclude their plan of reuniting Tsukuyomi with her lover and turning all living beings into third eyes. Seven years have passed since then.²³⁾ Koishi and a weakened Yukari are shown alive, separated, and left to reflect on the tragedy during a snowy Sunday²⁴⁾ in southern Germany.

As the 'Moonlight Descent Ceremony' requires absolute world peace, the Lunarians tried to absolve humanity of their sorrows by trapping these emotions onto the dark side of the moon,²⁷⁾ which had an unintended effect of Gensōkyō absorbing the 'madness' (狂気, kyōki). Eirin creates the 'detoxifying rain' (解毒の雨, gedoku no ame) as a temporary fix, but was ousted before she found a proper solution.

When the time came, Koakuma and Reisen experiment on the fairies,²⁸⁾²⁹⁾ then madness gets unleashed and turns everyone violent, but also falsified memories (e.g. Cirno's inability to remember,³⁰⁾³¹⁾ Udonge's legs³²⁾ being unharmed,³³⁾³⁴⁾ etc.). Overall, we're led to believe that this genocide was a Lunarian cover-up, and we're simply left wondering what our remaining protagonists will do with the vial that Kaguya gave them.