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With the outbreak of war, the Earth Alliance's Atlantic Federation begins a secret project to develop mobile suits to counter ZAFT's mass-produced ZGMF-1017 GINN as well as operate free of interference from the N-Jammers. The GAT-X303 Aegis Gundam is one of five initial designs that the Alliance secretly constructs with Orb. Unlike the other four Gundams, the Aegis Gundam is constructed with a different frame and can transform into a mobile armor mode. Like the other prototype Gundams, the Aegis Gundam is equipped with the new Phase Shift (PS) armor system. When in Phase Shift mode, the Aegis Gundam is nearly impervious to attacks from shell-firing artillery or melee weapons. However, use of Phase Shift for extended periods of time is a massive drain on the energy battery. In mobile suit mode, the Aegis Gundam's armament consists of head-mounted "Igelstellung" vulcan guns, four beam sabers and a beam rifle. However, in mobile armor mode it can use the powerful "Scylla" 580mm energy cannon. This powerful cannon is capable of destroying TS-MA2 Moebius units with one shot, and it can severely damage battleships as well.

The Aegis Gundam first enters combat on January 25, C.E. 71, when it is stolen by ZAFT pilot Athrun Zala during the attack on Heliopolis. During the attack, Athrun is shocked to meet his old friend Kira Yamato and see him end up as the pilot the GAT-X105 Strike Gundam. Though Athrun continues to fight against the Archangel, he always does so reluctantly and offers Kira several opportunities to join ZAFT. When Kira refuses to join ZAFT, Athrun vows no mercy for his former friend. As the Archangel continues to travel across Earth towards Alliance headquarters in Alaska, Athrun is sent down to Earth by Rau Le Creuset to pursue the ship. In a fierce battle on April 17, the Aegis Gundam is destroyed when Athrun self destructs the suit in a failed attempt to kill Kira. Afterwards, Athrun upgrades to the ZGMF-X09A Justice Gundam to pursue Kira and the stolen ZGMF-X10A Freedom Gundam.