Set in a parallel universe, the Earth and humanity have prospered enough to expand space colonies all the way into the arm of Orion in RayStorm. To maintain security, Earth imposes martial law, but a federation of colonies led by the colony of Secilia overthrows the Earths government and plans to obliterate the planet and all the people on it. To counter this, Earth sends out a covertly-developed fighter codenamed the R-Gray in hopes of penetrating the Secilian atmosphere and obliterating Secilias base of operations, the Juda Central System.

RayCrisis is set in a cyberspace environment and marked a style departure from the rest of the series. It details the events during which the supercomputer called Con-Human gained sentience and rebelled against its human creators. While the Earth is demolished to be remade as Con-Humans new corporeal form, a mecha-neurologist launches a desperate assault to jack into the supercomputers virtual core and cease its insanity. It is up to you to pilot the Waverider viruses and keep the malicious AI from causing any more chaos - even if it could be too late, you must ensure that no more lives are lost in the real world by stopping Con-Human in the digital realm.