Accelerator races back to the restaurant where he left Misaka Misaka passed out, only to find that she has been taken by Amai Ao. Fortunately Academy City has been thrown into a state of Lockdown and there is no way in or out, so Amai is unable to escape.
Accelerator hunts down Amai and the Last Order, but the virus in Misaka Misaka, originally thought to go off at midnight, turns out to be going off four hours earlier than planned. Without time to get Misaka Misaka to the lab to analyze and disarm the virus before it infects the entire Misaka network.. the only option is for Accelerator to kill the Last Order, otherwise the remaining 10,000 Misaka clones could all go berserk at once and start killing civilians.
Accelerator hypothesizes that he can use the vectors in the bioelectric pulses present in the brain to re-write the Last Order's programming to that of the clean, pre-virus state. With his focus entirely on reprogramming the Last Order, Accelerator is unable to use his power to deflect an incoming bullet straight to the head from Amai who shoots him in a last ditch effort to stop Accelerator from destroying the virus.
He is successful in reprogramming the Last Order before taking a bullet in the forehead, however he is able to focus his deflection ability at the last moment before it pierces his brain. Bleeding from the head, he confront Amai, acknowledging that while he did kill 10,000 sisters, and while he denies being any sort of hero, that doesn't mean the other 10,000 have to die either. Accelerator's wound is too grave though and he collapses in front of Amai. Before Amai can deal the killing blow, however, he is shot by Yoshikawa.