One day in Gensokyo, all of a sudden, there were lots of evil spirits going around. Reimu Hakurei, a Shrine Maiden and Marisa Kirisame, a black-clothed Magician were getting suspicious. They go into the underground to ask them to stop driving them to Gensokyo's surface. Depending on who you choose, one of them goes out to investigate.
The heroine starts to head underground, but runs into a Tsuchigumo, Yamame Kurodani who tries to stop the heroine from continuing. Yamame is quickly defeated and the heroine moves on. She moved on to a bridge leading to the Ancient City but runs into the bridge guard of jealousy, Parsee Mizuhashi, who also tries to stop the heroine from proceeding. Parsee is obviously defeated, and the heroine continues to go into the Ancient City. The Ancient City is populated by Oni ,therefore, encountering Yuugi Hoshiguma. After defeating Yuugi as a midboss, Yuugi starts following the heroine while shooting Danmaku. After, they battle and the heroine is victorious. Yuugi tells the heroine where the Palace of the Earth Spirits is. The heroine enters the Palace of the Earth Spirits and a cat is seen following the heroine. Later, the heroine meets the Master of the Palace of the Earth Spirits, Satori Komeiji. After Satori is defeated, she permits the heroine to go through to talk to her pets. The heroine proceeds to a much hotter place. She runs into a cat, Rin Kaenbyou. The cat transforms into her youkai form and is surprised to see a human make it all the way here. Rin tries to stop the heroine from proceeding to whom she describes as the most dangerous bird underground. Though, Rin is defeated. The heroine finally reaches somewhere even hotter than the place before. She makes her way but encounters Rin again. Rin states that if the heroine dies, she'll burn so hard she won't even leave any ashes. Rin attacks the heroine again, but is defeated. The heroine finally reaches Utsuho Reiuji, the most dangerous bird underground. Utsuho ate the god, Yatagarasu and claimed the nuclear powers. Utsuho states that with these powerful nuclear powers, she will take over the world above, which what made Rin Kaenbyou worried that she sent evil spirits into the world above. The heroine defeats Utsuho to stop her plan from taking over Gensokyo. After Utsuho's defeat, she states that it was Kanako Yasaka that whispered to her about swallowing Yatagarasu.
Some time after that, the heroine decides to pay a visit to the Moriya Shrine to find out more. While trying to find Kanako, she encounters Sanae Kochiya. Sanae is defeated and the heroine moves on until they suddenly found Satori Komeiji's little sister, Koishi Komeiji. Koishi asked where the goddess of the shrine is, but the heroine tells Koishi that they were actually doing the same. Koishi states that she went from all the way from the underground to up in the world above to visit this shrine. Koishi learnt that the heroine defeated her older sister, Satori. Koishi asked to fight the heroine because she was able to defeat Utsuho, so it must mean the heroine is stronger. After Koishi is defeated, on Reimu's story, Suwako Moriya, Moriya Shrine's true goddess appears. According to Suwako, Kanako is on a shopping trip. Apparently, Koishi wanted a gloomy power of love for her pets. For Marisa's story, after Koishi is defeated, Sanae Kochiya, a Shrine Maiden of the Moriya Shrine tells Koishi and Marisa that Suwako and Kanako are currently out.
