This article details the story of Mystic Square.
For no apparent reason, large quantities of demons and youkai begin to travel from Makai, the world of demons, to Gensokyo, swamping the land and leaving Reimu Hakurei with a lot of extermination to do. Frustrated, Reimu tracks the source of the invasion to "The Cave in Which the Door to Makai is Said to Be," which lies in the mountains behind the Hakurei Shrine. Reimu decides that it is her duty as a shrine maiden to root out the cause of this mess. Unbeknownst to her, Marisa Kirisame has learned of her plans and decides to follow along with the hope of discovering some unique powers to steal within Makai. Elsewhere, Mima, the evil spirit of the Hakurei Shrine, and Yuuka Kazami, the youkai, decide to travel to Makai as well, although they have their own reasons for doing so.
Within the cave, the heroine encounters the guardian of the gateway to Makai, Sara, and dispatches her with ease before beginning a high-speed flight through the boundary between worlds. Therein the heroine happens across a demon traveling in the opposite direction named Louise and crushes her as well. The heroine then arrives in Makai above a massive dark city, where she is confronted by Alice Margatroid, who attacks her with the help of her living dolls. After defeating her, the heroine flies away from the city and toward a grim fortress that rises up in distance. Along the way the witches Yuki and Mai appear and attempt to impede her progress, ultimately to little effect.
Entering the fortress Pandæmonium, the heroine soars past fantastic crystal designs while battling through legions of enemies. At the top she is met by a strange individual named Shinki who politely informs her that the demon invasion is entirely the fault of a civilian travel agency that is arranging tours of Gensokyo and that it lies outside of her jurisdiction. Before the protagonist can inquire as to the meaning of this they are interrupted by Yumeko, who adamantly insists that Shinki retire so that she may dispose of their uninvited guest. After defeating the maid, the protagonist meets Shinki again, who now explains that she is actually the god and creator of Makai itself. She promises to look into the tourist issue, but only after severely punishing the heroine for disrupting her realm so.
When Reimu defeats Shinki, she demands that she put a stop to all of the denizens of Makai coming to Gensokyo. Shinki promises she'll do something about it, but in the end, she brings the demons back to the shrine. It ends on a "well, it will always be busy at the shrine" note.
Marisa can't seem to figure out what her reason for coming to Makai in the first place was. Among her excuses are that she wanted to become the new god of Makai, that she's here on sightseeing, and that she's here to fool around. However, it seems that she grew quite powerful(and learned some tricks from her enemies), and while doing some extermination around the shrine at Reimu's request, the demons appear to be running away from Marisa without fighting.
Mima lies that she's a god of the human world, and then leaves out of boredom. Afterwards, she starts wondering if there might be a way to make herself a god, but eventually gives up, puts a sheet over herself, and goes to haunt the shrine.
Yuuka, also having been bored, explains that she likes picking on weaklings. She then decides to try and learn magic, but doesn't seem to get anywhere. Marisa, who had been watching, is greatly worried about what would happen if a youkai as powerful as Yuuka learned to use magic.
The bad endings after Shinki lightly taunting the heroine, has Reimu retreating to the demon-filled shrine then trying again without training, Marisa dragging Reimu to train with her, Mima chooses to harass Reimu some more. Yuuka in contrast talks about being tired and revealed she's talking to the player. She goes on to cutely tell the player to try again when they're ready and to choose her next time.
- Mystic Square/Story/Reimu's Extra
- Mystic Square/Story/Marisa's Extra
- Mystic Square/Story/Mima's Extra
- Mystic Square/Story/Yuuka's Extra
At an unspecified later date, the heroine again encounters Alice Margatroid, this time in a strange wonderland. Alice now possesses a large grimoire that grants her great magical powers and challenges the heroine to a rematch. After a lengthy battle and her second defeat, Alice laments her inability to defeat the heroine.
After defeating Alice, Reimu forces her to clean the shrine. Marisa takes Alice's grimoire, claiming that she will learn all the magic inside(which is supposedly impossible for humans to learn). Mima outright makes her a maid, and Yuuka takes her along for her magic training, though afterwards, Alice was able to return home, but with a sense someone was watching her (Yuuka).