Several months after
the destruction of Omega, Dr. Weil has assumed a dictatorial reign over Neo Arcadia, forcing many humans to flee. In response, Dr. Weil labels the escapees as
Mavericks and begins to purge them as if they were Reploids. A fleeing caravan led by a human journalist, Neige, is attacked by Dr. Weil's army. Zero, Ciel and a small band of Resistance fighters happen upon them and come to their aid. Neige explains they were en route to Area Zero,
the crash site of the space colony Eurasia, which has become one of the last places on Earth that can support human life. Shortly after parting ways, Zero learns of a plot called "Operation Ragnarok", meant to destroy all environments outside of Neo Arcadia in order to force humans to return and live under Dr. Weil's rule. Helping Dr. Weil on his quest are a group of violent Reploids called the Einherjar Eight Warriors. They are led by a military Reploid named Craft, whose motivations are conflicted due to a romantic history with Neige. The Resistance locates the Einherjar Warriors at various environmentally destructive facilities near Area Zero, and Zero sets out to eliminate them. After Zero defeats four of the Einherjar Warriors, Area Zero comes under attack from Neo Arcadia. Zero defends it and is forced to battle Craft. Neige breaks up the fight, but she is kidnapped by Craft, who escapes. Zero chases him to a prison where Neige is held and eventually rescues her. After Zero eliminates the remaining Einherjar Warriors, Ciel intercepts a radio message from Dr. Weil, who reveals that Operation Ragnarok was a ruse. The "true" Ragnarok is an orbiting satellite cannon, which he has activated to wipe out Area Zero. Before Dr. Weil can use it, Craft takes control of the cannon and turns it on Neo Arcadia in an attempt to kill Dr. Weil. Zero teleports to the station to stop Craft, but it fires before Zero can reach him, leaving Neo Arcadia in ruins. Zero defeats Craft, who succumbs to his wounds. Ragnarok unexpectedly begins falling out of orbit on a path headed for Area Zero. Zero infiltrates the core of the station and finds Dr. Weil, who survived the destruction of Neo Arcadia. Dr. Weil reveals that, while he is human, his mind was transplanted into a constantly-regenerating mechanical body when he was previously exiled, rendering him effectively immortal. Believing he can survive the impact of the crash and personally oversee the destruction of Area Zero, Dr. Weil fuses himself with Ragnarok's power core and attacks Zero. Zero defeats him, causing significant damage to the station, but Weil survives and fuses with the station itself. Zero chooses to stay on Ragnarok as it plummets into Earth's atmosphere and defeats Weil again, destroying the station utterly and neutralizing the threat of its crash. Ciel, the Resistance, and the refugee humans watch from Area Zero as falling pieces of Ragnarok burn up in the atmosphere, but Zero is nowhere to be found. Heartbroken, Ciel runs off alone and breaks down in tears, promising to carry on Zero's mission of maintaining peace between humans and Reploids. Zero's helmet, meanwhile, lies shattered in the desert among pieces of Ragnarok's wreckage. == Development ==