Operation Ragnarok (ラグナロク作戦 Sakusen na' Ragunaroku), is a large offensive campaign taking place over the course of Mega Man Zero 4, ordered by Dr. Weil in order to maintain his tyrannic rule and is perhaps the scientist's most heinous scheme yet.
With Copy X dead, Dr. Weil invokes Ordinance #8 and becomes leader of Neo Arcadia by unanimous vote. He then uses Neo Arcadia's resources as he sees fit, to gain control of Reploids through the combined powers of the Dark Elf and Omega, in order to punish the citizens of Neo Arcadia for his banishment. Although Zero destroys Omega, Weil remains ruler of Neo Arcadia.
It was for this reason that a Caravan moved from Neo Arcadia to Area Zero to escape from Dr. Weil's tyranny. Later, a mobile unit from the Resistance is stationed outside the area for protection. Dr. Weil, seeing Area Zero as a threat, decides to initiate a new campaign, "Operation Ragnarok", where all the nature outside Neo Arcadia and close to Area Zero will be destroyed and return to being an uninhabited wasteland, discouraging anyone from escaping his rule.
Weil's new generals, Craft and the Einherjar Eight Warriors, are sent on various missions, to disrupt nature's progress in Area Zero in various ways. Anticipating that Zero and his friends would try to foil his plans, Weil deliberately left the details of the campaign vague (Zero was none the wiser when Craft told him of only part of the operation). However, the Einherjar also serve as a diversion so no one would suspect that Dr. Weil is building a new weapon: the Ragnarok space station.
After Zero finished off Weil's forces to protect the habitat, Weil hacked into the Resistance's communication servers to boast the completion of Ragnarok, believing that they would wallow in despair since all their efforts have been in vain. Before Zero could do anything, the connection was interrupted by a transmission from Ragnarok itself. Craft, rebelling against Dr. Weil, has took manual control of Ragnarok, aiming its powerful cannon at Neo Arcadia in order to kill the despot.
The entire Resistance is deployed to rescue as many citizens from the city as they could, while Zero teleports into the station. However, right before he reaches the control room, the fully charged cannon has been fired, destroying the city in one blast. Even though Zero defeated Craft, the results still stand: casualties numbered over 20,000,000.
Before any grievances could be held, a second laser shot is fired, alerting everyone that Ragnarok is still operational, and is descending to Earth, preparing to crash into Area Zero. Zero heads back to Ragnarok to try and stop the collision, only to discover Dr. Weil, having survived Craft's attack, awaiting him at the core. The madman then fused with Ragnarok itself to battle Zero, but Zero defeats him, destroying Ragnarok in the process, presumably at the cost of his own life.
With Dr. Weil's demise and Zero's heroic sacrifice, peace has finally come back to Earth, leaving the survivors to arise and rebuild the sundered world. Centuries later, a new government would be established at Area Zero, becoming Cinq Ville, the largest city in the world.
Although Dr. Weil has been destroyed along with Ragnarok, his raw hatred allows his soul to merge with the fragments of Ragnarok to form the Biometal Model Ws. Other Biometals, based on Zero, X, and the Four Guardians are created to help worthy warriors continue the fight against Dr. Weil.