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Episode 1: A False Peace

In Cosmic Era (CE) 70, tensions ran high between the Earth Alliance and ZAFT (Zodiac Alliance of Freedom Treaty). After the 'Bloody Valentine' incident in which nuclear weapons were used to destroy the PLANT space colony Junius 7, all out war broke out. However, despite the fact that the Earth Alliance outnumbered ZAFT, the war dragged on for 11 months. In CE 71, 16-year-old engineering student Kira Yamato works on his laptop in the neutral colony of Heliopolis. He is visited by his friends Tolle Koening and Miriallia Haww, and they watch video of a ZAFT attack on the nearby colony Kaoshiung. Miriallia wonders if they'll be all right, but Tolle thinks that they'll fine because they're a neutral colony. As Kira's robotic pet bird Torii flies around, he thinks of the time when his friend Athrun Zala gave it to him. Nearby, an Alliance ship docks in Heliopolis, carrying ace mobile armor pilot Mwu La Fllaga and the five test pilots for the new secret Gundam mobile suits. The captain doesn't think that ZAFT will attack one of Aube's neutral colonies, and Mwu is sick of hearing that. In space, a Nazca class Vesalius and the Laurasia class ship Gamow hides behind an asteroid. On the Vesalius, a masked man named Raww Le Klueze discusses with the captain intelligence on the Gundams. Smaller vessels launch from both ships and head for Heliopolis. Kira, Miriallia and Tolle leave to visit Professor Kato and run into a girl named Fllay Allster, who is talking to two other girls about receiving a letter from Kira's friend Ssigh Argyle. A military officer named Natarle Badgiruel passes them and gets into an automatic car. Fllay and her friends get into an automatic car, and Kira and his friends get into one and head for the research center at Morgenroete. In space, ZAFT soldiers infiltrate the colony and head for the spaceport where the Alliance battleship Archangel is docked. At school, Kira meets with Ssigh, who is working on a robotic exoskeleton. Also in the room is a girl named Cagalli Yula Athha, a guest of Professor Kato. The ZAFT soldiers plant bombs all around the area near the Archangel and retreat. Cagalli tries to leave the room, and in space Raww gives the signal for the Vesalius to launch.

The Vesalius launches several GINN mobile suits as it heads toward Heliopolis. The Heliopolis government tells the ZAFT ships to not approach, but the ships are broadcasting interference waves. As the GINNs approach, Heliopolis sends out several Mistral worker pods to defend the colony. The bombs planted by the ZAFT soldiers explode, killing most of the Archangel's crew, including the captain. At the same time, Mwu launches in his mobile armor Mobius Zero and is joined by two Mobius mobile armors. The Mistrals and Mobiuses are all destroyed, but Mwu manages to damage a GINN. Several of the GINNs enter Heliopolis and begin attacking the city. The GINNs attack the area where Lt. Murrue Ramius is supervising the transport of the five prototype Gundams. Kira's friends evacuate the college, and he chases Cagalli when she runs away from the exit. The GINNs destroy all the Alliance ground forces near the Gundams. The ZAFT soldiers then fly down to the ground and attack Alliance soldiers with machine guns and grenades. Kira catches up to Cagalli, and he is surprised to see she is a girl. He asks her what she is doing, and she tells him she has to confirm something. The way back is now blocked, so Kira decides they should go to the factory and find a shelter. Kira's friends exit the college and find two GINNs fighting with ground artillery units. Kira and Cagalli emerge next to where the Gundams are. Cagalli shouts out that her father is a traitor, and Murrue shoots at them, thinking they are from ZAFT. Nearby, Dearka Elthman, Yzak Jule and Nicol Amarfi steal the Buster Gundam, Duel Gundam and Blitz Gundam. Kira convinces the people in a nearby shelter to take Cagalli in. While trying to find the other shelter, Kira warns Murrue that a ZAFT soldier is trying to shoot her. He tells Murrue he will go to the other shelter, but she says it has been destroyed. The area nearby explodes, so Kira jumps onto the Strike Gundam with Murrue. ZAFT pilot Rusty is killed, and Athrun rushes in and shoots Murrue in the arm. He flies over to kill her with a knife, but he stops when he sees Kira. He then escapes when Murrue starts shooting at him. Murrue shoves Kira into the Strike Gundam's cockpit and gets in. She breaks the Strike Gundam free of its restraints and gets it to stand up.

Episode 2: The Name Is Gundam

Murrue pushes Kira into the Strike Gundam's cockpit and gets into it. She manages to get it to stand, and nearby Athrun steals the Aegis Gundam. A GINN piloted by Miguel Ayman joins Athrun, and Athrun explains to him that the theft of the Strike Gundam failed. Miguel shoots at the Strike Gundam, and Murrue clumsily dodges the attack. Miguel pulls out his sword and tells Athrun that he will capture the Strike Gundam himself. Miguel moves in to attack, and Murrue activates the Strike Gundam's phase shift armor. Miguel hits the Strike Gundam with his sword, but the attack is ineffective. Athrun tells him that the Strike Gundam has phase shift armor and that his sword is useless. Missiles are fired at Athrun, and he destroys them with his vulcans. He then takes off to leave the Strike Gundam to Miguel. Miguel continues to attack with his sword and knocks the Strike Gundam into a building. Murrue gets up, and Kira sees that Miriallia, Tolle, Ssigh and Kuzzey Buskirk will be crushed if the Strike Gundam falls on them. He suddenly takes the controls of the Strike Gundam and pushes Miguel away. While Miguel is distracted, Kira quickly modifies the Strike Gundam's operating system. Miguel pulls out his machinegun and starts shooting at the Strike Gundam. Kira takes the controls and jumps into the air. He is followed by Miguel and pulls out his two Armor Schneider assault knives. He takes the assault knives and drives them into the GINN. Miguel pulls the self-detonation switch and flies out of the GINN as it explodes. Elsewhere, Natarle wakes up in the Archangel's hangar and finds most of the crew dead. In space, the Alliance ship loses control and crashes into Heliopolis. Mwu continues to fight and destroys a GINN. On the Vesalius, Captain Ades receives a message from Miguel about the Strike Gundam. Raww figures the situation must be serious if Miguel abandoned his GINN and decides to go into battle.

A signal is fired in space, and Mwu wonders why the GINNs are returning to their ships. Natarle explores the dock and finds some other survivors. Raww flies towards Heliopolis in his CGUE and wonders if Mwu can sense him in the same way he can sense Mwu. In the colony, Miriallia tends to Murrue's wound and bandages it. Murrue wakes up and sees Ssigh, Tolle and Kuzzey near the Strike Gundam, so she shoots at them. Kira tells her to stop, and she says they have seen the Alliance's top secret. At gunpoint she forces everyone to stand in line and tell her their names. Murrue says that since they have seen the secret they must stay with her until she gets orders. They refuse, and Ssigh says that Heliopolis is neutral and that they are just citizens. They ask what the Alliance is doing on Heliopolis anyway, and Murrue shoots in the air. She tells them that after what they have seen they can't remain neutral anymore. As Mwu searches the exterior of the colony, Raww attacks Mwu and heads into Heliopolis. Mwu follows and attacks Raww. On the Archangel, Natarle runs a diagnostic and sees that the ship wasn't damaged, but the port is destroyed. Kira tries to send them a message, but it is garbled in static. Natarle realizes that ZAFT is after the Gundams, so she decides to start up the Archangel and break out of the dock. A soldier named Arnold Neumann argues with her that they don't have enough personnel to launch the ship. Ssigh and the others find the Strike Gundam's trailer, which contains the Launcher power pack. Raww attacks Mwu from behind and destroys several of his weapons pods. As Kira prepares to attach the Launcher components, Raww breaks through into the habitable area and spots the Strike Gundam. He flies by the Strike Gundam and is attacked by Mwu again. He gets behind Mwu and destroys his linear gun. As Kira is about to go into battle, the Archangel fires its weapons and breaks into the habitable area of the colony

Episode 3: The Collapsed Homeland

Raww shoots at the Strike Gundam, but the phase shift armor deflects his attack. He then sets his sights on the Archangel, and Natarle has helmsman Neumann dodge his attack and fire missiles. Raww dodges the missiles, and the missiles hit the central core of Heliopolis and damage it. Kira grabs the Agni impulse cannon and fires at Raww, damaging the CGUE and blowing a large hole into the side of the colony. Raww is surprised that a mobile suit has such a weapon and escapes. The Archangel lands, and everyone is brought aboard. The bridge crew is surprised that a kid like Kira piloted the Strike Gundam. Mwu asks who is in charge, and Natarle explains that nearly everyone was killed, leaving Murrue in charge. Mwu asks for permission to come aboard since his ship was destroyed. He then asks Kira if he is a Coordinator, and when Kira says he is several soldiers point guns at him. On the Vesalius, Athrun works on the Aegis Gundam's OS. Raww returns to the ship and watches video of Miguel's battle with Kira. He tells Athrun and Miguel that the Strike Gundam and the Archangel must be either captured or destroyed. Athrun asks Ades to let him go, but Ades tells him to sit it out because Miguel has to release his frustration. On the Archangel, Tolle says that Kira isn't an enemy, and Murrue tells the men to put their guns down. Natarle asks what is going on, and Murrue says that because Kira is a Coordinator he was able to destroy a GINN and save everyone. Kira says that he is a first generation Coordinator, meaning that his parents' genes weren't modified. Mwu says that in the simulations the intended Gundam pilots could barely do more than move it. Heavy missiles are loaded onto the GINNs, and Nicol, Dearka and Yzak wonder what will happen next. Yzak thinks that it's ridiculous for Heliopolis to consider itself neutral. As repairs begin on the Strike Gundam and Mobius Zero, Kira takes a nap. Kuzzey wonders when Kira could have modified the Strike Gundam's OS. He wonders if Naturals can win a war against the Coordinators of ZAFT.

Murrue tells Natarle and Mwu that all the citizens have been evacuated to the shelters, which can separate from the colonies like escape pods. Mwu asks Murrue what she will do with the kids, and Natarle says they have to stay on board since they saw military secrets. Mwu says that there will be a big battle when they leave the colony, and Murrue thinks about using Kira as the Strike Gundam's pilot. Natarle disagrees and says that a mobile suit can't be entrusted to a kid, and she thinks Mwu should be the pilot. Mwu says he can't because Kira modified the OS in such a way that a Natural can't even handle it. On the Vesalius, Miguel launches in a new GINN along with two others piloted by Aurol and Matthew. Athrun takes the Aegis Gundam against orders, and Raww tells Ades to let him go because it might prove interesting. Murrue asks Kira to pilot the Strike Gundam when they are ready to leave the colony, and he refuses. He says he hates war and that's why he came to a neutral colony. The N-Jammers are used by ZAFT to block the radio, and Mwu knows that an attack is coming. He calls Murrue and says that she will have to be the captain. He says that although his rank is higher, he knows nothing about the ship. Murrue tells everyone to go to battle stations and asks Mwu if his Mobius Zero is ready, but he says no. Kira tells Murrue she is despicable and launches in the Strike Gundam, which has been loaded with the Sword type parts. The GINNs blast a hole into the colony and fly in, followed by Athrun. The Archangel fires its guns at the GINNs and accidentally damage the colony. Miguel carelessly fires his high energy gun at Kira and damages the colony's central core. Kira throws a beam boomerang to slice off the GINN's leg and then slices it up with his Schwert Gewehr anti-ship sword. The Archangel destroys the other GINN, but its heavy missiles are launched and destroy the central core. Kira and Athrun ask each other what they are doing as the colony breaks apart. Cagalli sits in one the shelters, which separates from the destroyed colony. As Heliopolis breaks apart, Kira is sucked into space.

Episode 4: Silent Run

Natarle calls Kira repeatedly, but he doesn't reply. He is shocked by the destruction of Heliopolis and wonders if his parents were able to escape. As he is about to return to the Archangel he sees a light from an escape pod and picks it up. Mwu asks Murrue what their next move will be, and she says they are still in battle and have to get out of the area. Mwu thinks that will be difficult with just the Strike Gundam and his Mobius Zero. Natarle suggests going to the asteroid port of Artemis, which belongs to the Eurasian Federation. Mwu thinks that the moon is too far, and Natarle is sure that Eurasia will understand their situation and give them assistance. Kira returns with the escape pod, and Natarle asks him who gave him permission to bring it in. She says they can't accept it, and he argues with her that it was drifting out of control. They continue to argue, and Murrue steps in and says she will accept the escape pod. After landing, the escape pod is opened and civilians are escorted out. Kira chases Torii around and sees that Fllay was in the pod. She asks him where they are, and he explains they are on an Earth Alliance ship. He takes her with him to see Ssigh and the others. On the Vesalius, Ades asks Raww what they will tell the council since a neutral colony was destroyed. Raww asks how Heliopolis could be neutral if it was developing weapons for the Earth Alliance. Ades says they have no mobile suits left to pursue the Archangel, and Raww suggests sending out the Gundams. Ades objects, and Raww says it doesn't matter since they already have the data on the Gundams. The Archangel sets course for Artemis and launches decoy missiles to confuse ZAFT radar. Raww examines the data and sees that they are heading for Artemis. Athrun lies down in his room alone and thinks about his dead friends Rusty and Miguel.

The Archangel continues on course for Artemis, and Kira's friends wonder where the ship is heading. Mwu comes down and tells Kira he will have to perform the maintenance on the Strike Gundam himself because of a lack of manpower. Kira asks why it's suddenly his mobile suit, and Mwu answers because no one else can control it. He tells Kira that if he has the power to do something he should, and they are the only two who can protect the ship. Kira runs off, and Fllay wonders what is going on. Ssigh and Kuzzey explain that Kira piloted the Strike Gundam and is a Coordinator. On the Vesalius, Athrun reports to Raww and is asked about what happened inside Heliopolis. Athrun explains that he was surprised to see his old friend Kira. Raww thinks that is very unfortunate and decides Athrun should be excused from the next battle. Athrun objects and says he wants to talk to Kira. He says that Kira is naive and is being exploited by the Naturals, so he thinks he can convince him to join them. Raww asks Athrun what he will do if Kira refuses, and Athrun reluctantly answers that he will shoot Kira. The Vesalius pulls in to a position parallel to the Archangel. Everyone goes to battle stations, and Mwu realizes if they stay still the Gamow will catch up, but if they start their engines the Vesalius will match their speed. Miriallia and the others decide they can't sit around while Kira fights, so they contact bridge officer Dalida Roe Laha Chandra and say they want to help. Kira sees them all in uniforms, and they say they will do their part while he fights. Kira puts on a pilot's suit to prepare for battle, and Mwu explains their battle strategy. Mwu launches in his Mobius Zero, and the Strike Gundam is loaded onto the catapult and outfitted with Aile type space equipment. The Archangel fires at the Vesalius, and both ZAFT ships launch their Gundams. Kira launches from the Archangel and heads into battle.

Episode 5: Phase Shift Down

Kira launches from the Archangel with the Strike Gundam's Aile pack. The Blitz Gundam, Buster Gundam and Duel Gundam phase shift and approach the Archangel. Kira encounters Athrun, and both pull out their beam sabers. Athrun tells Kira to put away his beam saber and says they shouldn't fight. He says they aren't enemies and asks Kira why he is fighting for the Earth Alliance. The other three Gundams begin attacking the Archangel, and Natarle fires missiles at them and deploys all the ship's cannons. However, the missiles have no effect. Yzak decides to help Athrun, and Dearka distracts the Archangel while Nicol attacks it from below. Kira tries to return to the ship, but Athrun blocks him and asks again why he is helping Naturals. Kira says he isn't with the Earth Alliance and is fighting only because he has friends on the Archangel. Yzak suddenly begins shooting at Kira, and Kira dodges his attack. As the Archangel evades the attacks from the Gundams, it moves into the range of the Vesalius. Raww tells Ades to fire as soon as the ship is in firing range. Undetected, Mwu travels through a debris field in his Mobius Zero and approaches the Vesalius. Kira pulls out his beam rifle and shoots at Yzak repeatedly, but he misses each time. Yzak uses his beam saber to slice into Kira's shield while Athrun watches from the side. Yzak asks Athrun to help him, and Kira continues to fire and drain his beam rifle's energy. Dearka and Nicol stop attacking the Archangel and join Yzak and Athrun in surrounding Kira. Mwu emerges from the debris field and launches he weapons pods. He damages one of the Vesalius' engines and causes it to spin out of control. After completing his attack, Mwu escapes to return to the Archangel. Raww orders Ades to withdraw.

Murrue tells Natarle to prepare the main guns and warn Kira and Mwu to get out of the way. The Archangel turns and fires its main guns at the Vesalius. Raww has the ship evade, but it still gets hit on the port side and suffers heavy damage. Raww sends an instant message to the four Gundams to return immediately. Yzak doesn't want to return until he shoots down Kira, so he presses the attack. Kira fires at Yzak, but the Strike Gundam runs out of power and phase shifts down. Yzak moves in to slice up Kira with his two beam sabers, but Athrun transforms and grabs Kira with the Aegis Gundam's claws. The other three Gundams follow Athrun, and Yzak asks Athrun what he is doing. Athrun says he is capturing the Strike Gundam, and Yzak reminds him their orders are to destroy it. Mwu sends Murrue an instant message to get the Strike Gundam's Launcher parts ready. Kira tells Athrun that he refuses to go to a ZAFT ship, and Athrun says that if he doesn't come he'll have to destroy him. Athrun tells Kira that his mother was killed in the Bloody Valentine incident. Mwu attacks Athrun and allows Kira to break free. Kira speeds toward the ship and is chased by Yzak. Engineer Kujiro Murdock sends out the Launcher parts, and Kira docks with them as Yzak fires a grenade at him. Kira fires the Agni cannon and damages the Duel Gundam. The Vesalius sends out a retreat signal flare, and the battle ends. After returning to the Vesalius, Yzak slams Athrun against a wall for humiliating them. Nicol tells them they shouldn't fight, and Athrun wants to be alone. Raww receives orders to return to ZAFT territory, and Mwu tells Kira he locked the Strike Gundam's OS so no one else can touch it. The ship approaches Artemis and is led in by an inspection ship captained by Biddulph. Armed soldiers surround the ship, and when Murrue asks what is going on, Biddulph tells her to be quiet.