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Throughout Tokyo, a frightening number of construction Labors have begun to suddenly go berserk and violently malfunction. The growing chaos of Tokyo is overshadowed by the looming edifice of the Babylon Project, the lynchpin of Japan's plan to reclaim the land under Tokyo Bay. To make matters worse, its lead architect recently committed suicide by throwing himself off of it into the waves below. How will the Metropolitan Police's Division 2 investigate the malfunctions in the midst of world-wide destruction, when the reliability of their own Labors lies in doubt?
Following the events of the first Patlabor movie, after a terrorist attack on a bridge in Tokyo, the whole country of Japan is in an uproar. The Japanese government suspects an attempt by the Americans to destabilize them, but in reality has no idea who is behind the attack. The only clues they have is of a secret organization called the National Defense Family, and the destruction of a United Nations Labor Unit. With time running out, the government calls upon Captain Goto and the Police Labor Force Division 2 to fill in the missing pieces...
Having defeated Logos and the Earth Alliance, the triumphant Chairman Durandal now reveals his ultimate plan for humanity. The world reacts with confusion and horror to the details of the Destiny Plan, but Durandal has come too far to let anyone stand in the way of his dream of eternal peace and happiness. Using the weapons of his fallen enemies, the Chairman demonstrates that he will stop at nothing to create his new world. The Archangel and its allies are now humanity's last hope to prevent Durandal from carrying out his plans. Once again, a fierce battle begins around the Requiem cannon and its relay stations, and the Gundam pilots meet in a final confrontation over the lunar surface. Shinn against Athrun, Kira against Rey, Archangel against Minerva... In the end, there can be only one victor.
Gathering their forces in the Mediterranean Sea, the Earth Alliance and Orb Union fleets launch a second attack on the Minerva, and this time not even the Archangel's intervention can halt the fighting. While Shinn unleashes his anger against the Orb fleet, Kira and Athrun confront each another in battle, and one of these lifelong friends falls in defeat. Back in the PLANT homeland, Chairman Durandal thinks back on his past and considers his plans for the future... plans which will require the removal of disruptive elements like Lacus and the Archangel crew. In the aftermath of the battle, Shinn reaches a fateful ecision. Stella, the enemy pilot he once promised to protect, is now a captive aboard the Minerva. Stella's physical condition is rapidly deteriorating, and Shinn will have to betray everything he believes in order to save her life.
The Minerva docks at a ZAFT base, where they are met by Chairman Durandal. Over a quiet dinner, he talks with Athrun, Shinn and other members of the crew. This conversation leads Shinn to reflect on the past, and the events that brought them to where they are now. But understanding does not bring peace, and after another argument with some of his shipmates, Shinn heads ashore to clear his head. There he meets a beautiful girl, and watches her fall into the ocean. He dives in to rescue her, and in turn then must wait to be rescued. Meanwhile, the Alliance Forces gather, along with their Orb Allies, to launch an attack on ZAFT. The Minerva scrambles and prepares for battle. But unknown to either side, far beneath the waves, another group is going to try to put an end to the fighting.
The year is Cosmic Era 73. The Bloody Valentine War, fought between the PLANTS space colonies and the nations of the Atlantic Federation, has ended and an uneasy truce has settled upon the Earth sphere. With the signing of the Junius Seven Treaty, the world's soldiers have left the battlefield and the grizzly sights of war behind. Many who fought now seek peace and refuge in the shelter of civilian life. But one boy, Shin Asuka, is finding that incredibly hard. A coordinator who lost his entire family during the Battle of Orb, he now fights with ZAFT in one of their newest machines, the Impulse Gundam. Of course, ZAFT is only developing these machines for defensive applications - or so they claim - but when a group of Federation operatives steal some of these prototype machines, the world is once again plunged towards war.
The official music video for Mobile Suit Gundam: The Witch from Mercury's opening theme Shukufuku, performed by YOASOBI.