On the day Tōma Kamijō 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, Tōma wonders. In the chaos of Stiyl's attack, he tells Tōma, Index and Arisa that she might cause a war between the magic side and the science side.
In the year 3195, there was a war between an army of robots and the humans. When Shaian, a sentient combat armor, lost his companion in battle, he shut down until his internal systems spotted a new human. It's now almost a 1000 years later, and Shaian's greatest enemy is still alive and doing battle in Brazil. With a new friend's help, Shaian may be able to stop this evil force before another war rages over the continent.