After becoming the pilot of the Strike, Kira often had to confront his childhood friend Athrun Zala, a ZAFT soldier. While Athrun was driven to fight to protect his nation, Kira was more concerned about his friends who were forced on board the Archangel, whose officers decided not to surrender the ship.

During his first space battle, Kira overused the Strike's power supply, disengaging the Phase Shift, forcing him to soar away from his enemies. However, Athrun/Aegis catches him, intending to bring his friend to the Gamow, stating that he is a Coordinator and belongs with his own kind. Luckily, the timely save from Mu La Flaga spares Kira from capture. He then makes it back to the Archangel to began equipped with the Launcher Striker to fend off ZAFT.

When Flay Allster, Kira's friend from Heliopolis, witnessed the death of her father by ZAFT hands, she started to discriminate Kira as a Coordinator. In emotional distress, at first she faked affection for him and eventually slept with him in order to make him kill all the Coordinators on her behalf.

This contributed to his decision to officially become an Earth Alliance soldier. Soon after the destruction of the 8th fleet, a fleeing ship of survivors from Heliopolis accidentally crossed in the middle of his fight with the GAT-X102 Duel. The pilot of the Duel, Yzak Joule indiscriminately shot down this ship during his battle with Kira. Kira tried in vain, but ultimately was unable to stop Yzak from destroying the ship. This event would continue to haunt him for a long time. Flay's influence would drive him to use a more violent fighting style against the ZAFT forces who engaged the Archangel at the Desert in North Africa and the ones at the Indian Ocean.

Kira later ended the relationship, after deciding that he and Flay were not right for each other. Soon, while again en route to the Alaskan Base JOSH-A, the Archangel is attacked by ZAFT forces, led by Athrun. During the initial skirmish, Kira damaged Athrun's Aegis unit, and killed Nicol Amalfi, a friend of Athrun's and pilot of the GAT-X207 Blitz. Kira would soon face another confrontation with Athrun, prior to which he and Flay briefly reconciled in a hallway, deciding to spend time together "later." Throughout the battle, Flay privately expressed concern for Kira, indicating that her feelings for him had become genuine. The confrontation ended in a draw, though the GAT-X105 Strike unit was destroyed and Kira was seriously injured. Although many believed he had died, he woke far away on PLANT, in the mansion of Lacus Clyne. It turned out that he had been pulled from the wreckage of the Strike by Junk Guild member Lowe Guele, who turned him over to the care of Reverend Malchio, a family friend of the Clyne family (Kira later had the opportunity to thank Guele when ReHOME delivered supplies for the Three Ships Alliance later in the war). However, it is during this time Lacus developed an affection towards Kira. To assist Kira to end the fighting, Lacus stole and gave to Kira the ZAFT ZGMF-X10A Freedom prototype. Kira then returned to Archangel with the stolen MS. Following the Battle of JOSH-A, Archangel defected to ORB and later to the Clyne Faction. In Orb, Athrun joined the Archangel after defecting from ZAFT and brought with him the brother unit of the stolen Freedom, the ZGMF-X09A Justice.

Eventually Archangel, the ORB ship Kusanagi, and the Clyne Faction's stolen ZAFT ship Eternal, , formed the Three Ship Alliance, supported by Kira's stolen ZGMF-X10A Freedom and Athrun's ZGMF-X09A Justice units. This new group received assistance from the Junk Guild, and the prototype Archangel tender ship turned Junk Guild vessel ReHOME served as a tender ship for the TSA.

Towards the end of the Bloody Valentine War Kira learned that he was the Ultimate Coordinator; his fetus was artificially developed outside his mother's womb, and all his genetic enhancements were exactly as they were intended to be. He was the first and the last fetus to be successfully developed using the apparatus. Kira also learned that he was the twin brother to Cagalli Yula Athha, but she was born naturally. It has also been suggested that the only "failed" subject to survive, Junk Guild MS pilot Canard Pars, is also Kira's older brother, but these rumors have yet to be proven. However, the two met shortly after the war was over; Canard was about to kill Kira, when he stopped, looked into Kira's eyes, and decided to abandon his quest to kill Kira.

Kira, Athrun, Lacus, Cagalli and the Three Ships Alliance helped in ending the Bloody Valentine War. In the final battle at Jachin Due, Kira witnessed the death of former lover, Flay Allster, at the hands of the ZGMF-X13A Providence, piloted by Rau Le Creuset. Driven by transcendent anger and hatred, Kira managed to overcome the Providence Gundam's DRAGOON system and mortally wound Rau with his beam saber. Shortly thereafter the Providence was completely destroyed by a misfiring of the GENESIS doomsday gamma laser. The Freedom itself was seriously damaged during this battle.

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Gundam SEED Destiny takes place two years after the war, where Kira and Lacus lived in an orphanage in Orb, run by a Clyne family's friend, Reverend Malchio. It is mentioned that their relation is lovers started from episode 13 of Gundam SEED Des...

While lacking any true form of military training, Kira's fighting ability has developed much as the series progresses along with his ability to go into SEED mode. In the original Gundam SEED series , Kira is shown to be inexperienced with handgun...

Kira is a pacifist; he dislikes war but he will protect those who are important to him. He became more active when the Archangel went back to battlefield, where with his Freedom he avoided hitting the cockpits of enemy MS, and only disabling them. He...

i manga är det inte höst då råsa löv faller från träden det är vår...