Da Capo II centers around Sakurai Yoshiyuki and his romantic relationships with six fellow students of Kazami Academy. Kazami Academy is a combined middle and high school on the small but mysterious Japanese island of Hatsunejima. The island is host to magical sakura trees that bloom all year round. Several of its residents also have various magical abilities.
The game's structure follows a three act setup, each act has multiple possible scenarios based on player choices. Act one follows the lead-up to the academy's culture festival and the protagonist's class can either perform a puppet show or set up a haunted house display, with either choice resulting in being able to interact with a different set of heroines. In this act, dialog choices are minimal and most player choice comes when selecting which girl to interact with via a map screen. Act two takes place during the short winter break, with three possible scenarios depending on who you befriended in act one. This act contains many dialog choices and these choices determine who you hang out with. Act three contains the unique chapter for whichever heroine you became romantically involved with. There is very little to no interaction in this act.