One day while Shirou is delivering a secret device to his colleague, he meets Amane Mao, a super-strong girl capable of lifting cars. This device, the VITA system, is a new weapon theoretically capable of defeating ERRORs: a breed of enormous, cybernetic mutants that necessitated the use of weapons of mass destruction on Old Tokyo fourteen years ago.

Suddenly, one such ERROR appears before the two and goes on a rampage. Shortly after a failed argument to convince his colleague to approve use of the VITA system simply to save civilians, his colleague is devoured by the ERROR. Faced with death, Shirou has no choice but to accede to Mao's request to activate the super-weapon and destroy the ERROR.

...and thus Shirou's eventful days as the male master of the VITA system at St. Liddel's Girls' Academy are about to begin...

(Source: AnimeSigma, edited)