Special conditions: This works on Gensokyo is a place that has its own environment, time and even seasons, time passing is an illusion here, progress is an illusion in itself because the seasons change.
In a somewhat unmentioned passing of a future, what may seem like 20 years later passed, but in Gensokyo, the equivalent of around 1 year barely passed since the UFO incident.
Humanity has been consumed by a great disease, genetically engineered to consume the sanity of all man and the ability to think, no human has been spared. Its true identity is unknown, nor is it known who was the culprit, but on a survivor which dropped to Gensokyo after what appears to be one year when Gensokyo's population needed to be checked by 'Yukari's Spiriting Away Team'... Yukari realized something grim....
There are no humans she can grab within Japan's distance.
The Spiriting Away Team, like the namesake, is Gensokyo's team of Yukari's extended network of servants living in her gap universe which takes away humans from around Japan during specific times of the year to replenish the population. When the servants reported "there are no people in Japan" Yukari worries, and reports to Reimu.
At first like all known occasions Reimu didn't care... until Yukari mentioned... "Imagine, someday you are gonna have to learn how to speak English..." Her spine shivered... "No way", "Yes, you will..."
What say we go solve this situation?
With Yukari's help, they traveled out, the world however, has already left the reigns to the wind, dark skies and tumbling storms, crushed buildings and empty streets...
What happened to humanity is an enigma, and although Reimu and Yukari is immune to the disease, tagging along Marisa and Nitori and just in case Gensokyo correspondent doctor/medicinal advisor Eirin would have to rely on the timebomb method. Only a small vial of antivenom has been extracted from the survivor which they caught earlier, that small vial can save one of the people tagging along. It wasn't sure if Kappa are immune, or that Lunarians actually should need to fear, but Marisa is 100% human and capable of the disease.
In a ruined Japan, they march, looking for survivors.
Suddenly like a jolt, a foreign presence emerges...
She has a tall black hat, with two eyes attached to each side a small frame of a body, yellow frogs attached to a black and red blouse and a dark orange sleeved inner dress. She rode a giant frog towering and dwarfing all of them ahead...
"Greetings... my name is Kowasu Yarimo, I am the Anti-God of the lands of Japan..."
What has happened... will be unfolded.