In Gensokyo, people relax and bask in the calm of a winter without end. Spring has shown no sign of arriving even though it's already May, and in fact the snowstorms are continually getting worse. Reimu Hakurei, a shrine maiden of the Hakurei Shrine, is tired of being cold day in and day out and wants to find the source of this unnatural weather. Marisa Kirisame, a black-clothed magician, sees a cherry blossom petal float down outside her warm house and wonders if spring is happening somewhere else. Sakuya Izayoi, the maid leader of the Scarlet Devil Mansion, knows that their winter supplies are diminishing quickly, and wants to end this prolonged winter before they run out completely. Depending on who you choose, only one of these three heroines actually goes out and investigates.
The heroine starts off her journey by heading off into the snow-covered forests in search of clues. She battles the ice fairy Cirno and the winter spirit Letty Whiterock in the forest, and the nekomata Chen in the village of Mayohiga, without any progress in her search. Finally, after defeating Alice Margatroid and her dolls, the heroine finds a lead when she notices several cherry blossoms blowing around in the sky. The heroine follows the trail of cherry blossoms high above Gensokyo, breaking through the greetings of Lily White, eventually reaching a great magical boundary and the poltergeist musicians Prismriver Sisters. After silencing the Prismriver Sisters, the heroine crosses the boundary into the Netherworld.
After fighting off several ghosts, the heroine is confronted by human-ghost gardener Youmu Konpaku. Youmu explains that she had been stealing the essence of "spring" throughout Gensokyo in order to make the Saigyou Ayakashi, a youkai cherry tree, bloom perfectly with the rest of Hakugyokurou's gardens, as per her master's orders. The heroine defeats Youmu and hurries to Hakugyokurou to get Gensokyo's spring back. Now at the end of a long journey, the heroine comes face to face with Yuyuko Saigyouji, the ghost princess of Hakugyokurou. Yuyuko reveals that she wanted to revive a certain soul that has been sealed within the Saigyou Ayakashi from before her existence. In order to break the seal, the youkai cherry blossom tree needed to bloom fully and completely. Yuyuko and the heroine wage a fierce battle, to get the last "spring" contained in the heroine needed for the Perfect Cherry Blossom, and to reclaim Gensokyo's spring, respectively. After the heroine defeats Yuyuko, the Saigyou Ayakashi starts to lose its health. However the seal has been weakened from the near-complete bloom, and the sealed soul is temporarily unleashed. The soul is actually Yuyuko's. The heroine dodges attack after attack until Yuyuko's soul is finally sealed once more.