Akira has returned alive after defeating Beta, but soon Tokyo is targeted by a large-scale hacking attack. He dives into the network along with Ygg's clones to figure out the cause, and fights the enemies within, but in the meantime the hacking spreads to the entire world.

It takes over military bases and fires a volley of ICBMs, seeking to destroy the entire world. In order to save humanity, Akira makes a decision born of love.
Minami, remember what you said 
back when we first met?
مينامي، أتذكرين ما الذي قلتِه
عند لقائنا الأوّل؟
Minami, ¿recuerdas
qué me dijiste al conocernos?
Minami, ¿recuerdas
qué me dijiste al conocernos?
Minami,
Minami.
Minami, se lembra do que me disse
na primeira vez que nos encontramos?
Минами. Помнишь, что ты сказала
при нашей первой встрече?