When humans on the Outside World began losing their faith in her and Kanako Yasaka, the shrine's actual deity, Kanako decided to move the shrine to Gensokyo where at least youkai might have faith in them. During the events of Mountain of Faith Sanae tried closing down the Hakurei Shrine in order to establish the Moriya Shrine as the dominant one, not realizing how powerful humans like Reimu Hakurei and Marisa Kirisame were. In response to the threats Sanae was defeated by the heroine followed shortly after by Kanako and Suwako Moriya's defeat. However, the residents of the Moriya Shrine have since come to an understanding with their new neighbors and live in peace with the other residents of Youkai Mountain.
Following the extra scenario as the player heads through the Moriya Shrine to look for the two goddesses, Sanae appears as the midboss of the stage. She believes that the traditional greetings in Gensokyo is by attacking with danmaku because you can't be trapped by common sense. She attacks the heroine with three spell cards, but was defeated. Specifically on Reimu's and Suika's scenario, she returns stating that Kanako was creating a kappa industrial revolution by using the old Remains of Blazing Hell. She was unaware of the incident that occurred in the game, making Reimu unhappy.
In each scenario of Undefined Fantastic Object, Sanae is ordered with a different task. Depending on this, her secondary bullet will become a snake or a frog.
Kanako Yasaka's task is to train her own abilities by hunting Youkai.
- Main article: Undefined Fantastic Object: Sanae B's Scenario
Suwako Moriya's task is to find the Treasure Ship.
Sanae notices the strange spirit at the Moriya Shrine in Ten Desires and knows what they are: divine spirits, born from humans due to powerful fears, desires and feelings. She takes the opportunity to gather the divine spirits, as it is the same as gathering faith from humans. She can't, however, figure out why all these divine spirits have appeared in the first place.
The Curiosity Mars rover appears in Gensokyo, causing all life around it to become petrified and turn to stone when it gets too close. Left unchecked, Curiosity would eventually purge all life from Gensokyo. Kanako and Suwako send Sanae to investigate it, which eventually leads Sanae to outer space and to the Lunar Kingdom, where she learns that Curiosity was sent to "purify" Gensokyo and make it inhabitable to the Lunarians, due to an external threat the Lunarians are facing. Sanae is forced to save the Lunarians, lest Curiosity continue its destructive path.
At the request of Kanako, Sanae is sent to investigate the proliferation of Ability Cards on Youkai Mountain.
Because of the opening of the marketplace, ownership of the ancient land was lost. This has caused greedy animal spirits to attempt to claim ownership of the land.
Sanae is told to investigate the spirits flooding the surface, so she leaves the shrine after defeating Tsukasa Kudamaki, who wanted Sanae to lend the shrine. She then fights Ran Yakumo and Mamizou Futatsuiwa following her orders of attacking every beast youkai she encounters to solve the incident. The tanuki then affirms that the shrine maiden doesn't understand the nature of the incident at all and gives her directions to solve it, which only led her to Hell. There, she fights Yachie Kicchou, who admits that she has an “ally” in the Forest of Sanctuaries. After defeating said ally there (Son Biten), Sanae falls in Biten's trap and ends up fighting Zanmu Nippaku.
At the end, she fails to put an end to the beasts' and Zanmu's plans, but she at least earned a new ally.