Kisaragi Amatsuyu is invited out alone by the cool beauty upperclassman Cosmos and his childhood friend Himawari. Expecting to hear their confessions, he triumphantly goes to meet each of them in turn. But Cosmos and Himawari both instead confess to Amatsuyu that they like his friend. Amatsuyu fights this lonely battle, but there is another girl who is looking at him. She is a gloomy girl with glasses and braids. Amatsuyu finds that he hates her, because she's always turning her sharp tongue only on him and finding enjoyment in his troubles. But it turns out that she's the only one who actually does like him.

On the day Touma Kamijou and Index see Academy City's space elevator, Endymion in the distance, they meet a Level 0 girl with an amazing singing voice, Arisa Meigo. As the three enjoy their time together after school, magic-user Stiyl Magnus suddenly attacks them. His target: Arisa. Why would a girl from the science side be targeted by someone from the magic side, Touma wonders. In the chaos of Stiyl's attack, he tells Touma, Index and Arisa that she might cause a war between the magic side and the science side.