Dormant, experimental cells begin to awaken inside their human hosts, turning them into creatures called 'Amazons'. Two Amazons- Jin Takayama and Haruka Mizusawa- transform into Kamen Riders Amazon Alpha and Amazon Omega, aiming to exterminate the growing threat.

This is the love story between Chihiro, a boy raised by an Amazon, and Iyu, a girl brought back to life with the help of Amazons. It's far more than a mere, heart-warming "boy meets girl" love story. The focus has moved from the turbulent ending of Season 1 to five years later.