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After repeated and expensive attempts to seize power through brute force fail, Cobra Commander comes up with a new plan to recover its financial investments and at the same time seize control of world power. The plan begins with the seizure of the High Frequency Active Auroral Research Program array (HAARP), which superheats the ionosphere. Following this seizure various rockets carrying electronic equipment are launched into low earth orbit. A solar powered stratellite network is deployed just below the ionosphere, allowing Cobra to maintain a covert worldwide communication network. Finally, at a decommissioned nuclear missile silo in Siberia, a prototype particle beam weapon is unveiled and powered up. As a show of how serious he is to his own troops, Cobra Commander kills Major Bludd and has his dead body found in Washington DC. He warns them he will tolerate no attempts against him.
With these pieces in place, the Cobra operative known as Firefly fires a special missile package through the wall of the United Nations building in Manhattan, NY, the missile deploys a small holographic projector. Cobra Commander then uses the holographic projector to make a broadcast to the assembled UN representatives in which he demands that all nations on earth turn control of their resources over to the Cobra organization within 24 hours, or face indiscriminate attacks upon their capital cities. As a show of force, the cannon is fired at Moscow, Russia, wiping the city off the map and killing approximately ten million men, women, and children by disrupting their atomic and molecular structures.
In the Pacific Ocean USS Flagg, a modified aircraft carrier that serves as the base of operations for all G.I Joe activity, falls prey to a saboteur. Explosives rigged in the armory, flight deck, bridge, and other vital areas destroy almost all on board weapons, ammunition, and vehicles in addition to severely compromising the vessel's integrity, leaving the Joes at a disadvantage. A check of the vessel reveals that a Joe named Bazooka, who was supposed to have been on guard duty, had been killed prior to the attack. An autopsy performed by Doc uncovers a note hidden in Bazooka's mouth which reveals the assassin and saboteur to be Storm Shadow, a former friend of Snake Eyes from his days as a ninja in training. Snake Eyes, after reading the scroll's hidden note, departs to take on Storm Shadow and settle their rivalry once and for all.
Meanwhile, the other Joes onboard the Flagg set about analyzing the situation. They learn from Dial Tone that satellite communications are down due to the superheated ionosphere, and eventually trace Cobra's activity to the HAARP array, the Satellites, and the Siberian particle cannon, which lies beneath the decommissioned Russian ballistic missile complex. Logistical personnel explain that the HAARP array allows the particle cannon to superheat the ionosphere causing it to reflect particles, the energy from those charged particles is dispersed across the super hot ionosphere, and then reassembled above its intended target. Once there, the particles are focused into a powerful collimated beam that uses charged particles to wipe entire cities off the map.
Three separate Joe teams are deployed: The first team consisting of Gung-Ho, Roadblock, Stalker and Beachhead manages to recapture the HAARP array in Alaska and free hostages being held by Destro and the Baroness. The second team consists of Ripcord, Duke and Scarlett, Duke and Scarlett perform a HALO jump to the Siberian facility wearing winged jet packs, they infiltrate the location, kill Zartan, and destroy the location by forcing the repurposed nuclear warheads powering the particle cannon to detonate. Tunnel Rat manages to knock out Cobra's orbiting stratellite network by reviving technology from Project Manhigh, building an assault platform capable of reaching the stratellite array without activating each stratellite's defensive cannons. He then uses a microwave power transmission broadcast via the stratellite's rectenna to compromise and destroy the network. However, Cobra Commander unveils a second smaller HAARP array on an islet in Micronesia, and a second lesser particle cannon hidden in the town of Springfield, a major Cobra installation. Cobra fires this secondary particle cannon at the Flagg, sinking the already evacuated carrier. Elsewhere, Snake Eyes and Storm Shadow meet on an island with an abandoned complex that was once used to train the ninja clan Snake Eyes belongs to. In flashbacks, Snake Eyes recalls his time as a student and how he attempted unsuccessfully to prevent his mentor's assassination at the hands of a Cobra mercenary working for Storm Shadow. Snake Eyes and Storm Shadow engage in a fight to the death, a fight that ends with Storm Shadow's defeat.
Over the Pacific Ocean several aircraft of various types carrying the evacuated Joes and crew members of the Flagg arrive at the location of the secondary particle cannon. After exchanging lethal fire with entrenched Cobra forces, Flint and Scarlett manage to create an opening, allowing Duke and Snake Eyes to gain access to the facility, Duke makes his way to the control center and discovers that Cobra Commander ordered his men to set the particle cannon to fire at Washington, DC and then slaughtered them, and has locked himself inside a breach proof safe room within the control center. Unable to reach Cobra Commander and prevent the firing of the particle cannon, Duke elects to reprogram the targeting coordinates, causing the directed-energy weapon to fire on its own location. Cobra Commander is apparently caught in the blast and killed since he was not able to escape from his room. However, in his debriefing on the incident, Duke notes then when the G.I. Joes returned to the site, Cobra Commander was missing from the bunker's ruins, suggesting he survived the destruction of Springfield.
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