Rikuto had a new younger brother Ayumu after his father’s remarriage. However, little did he know that Ayumu was actually a girl and it was under her mother’s orders that she pretend to be a boy to him. Every day, his heart beats a little faster around his overly cute brother (sister), while her heart aches in having to hide her true identity from her kind brother.
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With the arrival of spring, Rikuto and Ayumu begin attending the popular private school Asaoka Academy, with Ayumu dressed up as a girl. As Rikuto becomes friends with his classmates, he notices that they all have something missing. His friend from middle school, Matsuri, has lost sight of what it meant to be a girl. The cool-mannered Mao dresses as a boy even though she is a girl. The extremely shy class rep Kimika wishes to change herself. With Ayumu by his side, he sets out to help them seek out what they are missing.

Koi to Senkyo to Chocolate follows the protagonist Yuuki Oojima, who attends Private Takafuji Academy, a large school with over 6,000 students. Yuuki is a member of the food research club, along with seven others, including his childhood friend Chisato Sumiyoshi. The members leisurely spend their time in the club not doing much activities. When the election of the next student council president comes up, the front runner Satsuki Shinonome proposes that clubs that have no merit should be sorted out and abolished. The food research club seeks advice from the current student council president Yakumo Mori, who suggests Yuuki run in the election as an opposing candidate. Yuuki learns about the issues facing the school and decides to run in the election.

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