Disclaimer: I do not own Gundam SEED, the GM's or any of the characters from the series.
Note: This story starts just after Heliopolis is destroyed, and does not follow the show's timeline.
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Prolougue
It was a normal day in the space colony of Heliopolis, with everyone going about their daily activities. That is, until sirens started to wail and explosions started going off. The unthinkable had happened: ZAFT had attacked a neutral colony! Kira Yamato and his friends rushed to the evacuation space pods, but Kira and another girl got separated in the confusion. They finally found a pod, and it just happened to have two spots left. (In the series, it only had one, and Kira had to go find another, and this eventually led to him getting the Strike.) So Kira and his friends escaped Heliopolis, never to appear in this story again.
Meanwhile, the Archangel was badly damaged in the explosion that started to attack. The only survivors were Murrue Ramius and Mu La Flaga.
At the same time, Athrun Zala, Yzak Joule, Dearka Elsman, Nicol Amalfi, and Rusty Mackensie steal the 5 prototype Gundams that the Earth Alliance secretly produced in Heliopolis. When Rusty went to steal the Strike Gundam, he had to fight Murrue Ramius, who had taken up a position beside the Strike's cockpit. After being wounded in the right shoulder by Rusty, she slipped and fell into the cockpit. When Murrue fell, she hit her head on something and was knocked unconscious. Rusty quickly climbed into the cockpit after shoving her to one side. After getting the Gundam on it's feet, the Coordinator took off after the rest of the team. Besides the Strike Gundam, the Duel Gundam, Buster Gundam, Blitz Gundam, and Aegis Gundam were also stolen.
Mu La Flaga had managed to get into space in his Moebius Zero and was fleeing the area. His Mobile Amour was also damaged in the explosion, and he couldn't afford to stay and fight. La Flaga had to alert the authorities of the attack.
Waiting in space for Athrun and the others was Miguel Aiman. He was fighting off the remaining attack force of Heliopolis, which consisted of a large group of Moebius Mobile Amours. After finishing off those, Miguel joined up with his teammates and headed back to their ship.
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I know it's short, but the prologue gives a quick overview of what happened. I may include Mu La Flaga in a later chapter; I'm still thinking about it. And yes, I'm using the English names.