Mystic Square allows the player to select from among four unique protagonists, each hailing from one of the 2 prior danmaku shooting games in the series. Series mainstays Reimu Hakurei and Marisa Kirisame are joined by former enemies Mima and Yuuka Kazami for a journey reaching to the depths of the Makai. Mystic Square also marks the first appearance of Alice Margatroid as an opponent, who later stages a comeback in Perfect Cherry Blossom.
Although limited by the PC-98 hardware, Mystic Square is the most refined of the PC-98 Touhou titles, and features gameplay quite similar to Windows Touhou games. It employs a variant of Lotus Land Story's Dream Bonus system, rewarding the player for taking risks (i.e. collecting point items from the top of the field area). Its rank system, however, is more lenient than Lotus Land Story's.
