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 Destiny. As the events escalated to the Second Bloody Valentine War, the orphanage was destroyed by unknown forces trying to assassinate Lacus. The attempt on Lacus' life convinces Kira to once again pilot the rebuilt Freedom and participate in combat, despite his reluctance to do so. Kira and Lacus returned to the Archangel and escaped from Orb, as the island nation entered the Earth Alliance. Before leaving Orb, Kira kidnapped Cagalli from her arranged marriage with Yuna Roma Seiran, despite Cagalli's objections at first.

From there Kira continued to fight in the rebuilt ZGMF-X10A Freedom. His first sortie with the Archangel rogue faction was in the Dardanelles for the purpose of stopping the EA/Orb offensive against the ZAFT battleship Minerva. Upon his arrival, Kira destroyed the Minerva's main "Tannhäuser" cannon, which was fully charged an therefore caused large damage to the ship, killing several crewmen. Then he proceeded to disarm any mobile suits on both sides which fired at him, but in the end he provoked the death of ZGMF-X2000 GOUF Ignited pilot Heine Westenfluss. He continued to distrust ZAFT, even after he learned Athrun's support of it in his meeting with Athrun, Cagalli and Miriallia in Crete, and also intervened in another EA/Orb battle with the Minerva in Crete, where drove by anger he destroyed (or damaged beyond repair) Athrun's ZGMF-X23S Saviour.

He also went to Berlin to fight against the might of the GFAS-X1 Destroy, and was eventually joined by the Minerva, along with Shinn Asuka's Impulse Gundam, where he defeated Stellar Loussier, by stabbing his beam sabers and its chest, where the cannon was located. The resulting explosion killed Stellar. Unfortunately, his actions had already gained him an enemy, Shinn Asuka, a former Orb citizen who joined ZAFT after his family was killed in the assault on Orb by the EAF during the first war, but after Stellar's death, Shinn's dislike for Kira and Freedom Gundam turned into hatred. In the following battle, Phase 34, upon the orders of Chairman Dullindal, the Freedom was attacked and destroyed by Shinn and his ZGMF-X56S Impulse mostly due to Shinn's knowledge of Kira's unwillingness to kill. Kira was able to survive the explosion with relatively minor injuries by using an emergency cutoff control to shutdown the Freedom's nuclear reactor before it went critical. Then, the destroyed Freedom, sank into the ocean before being rescued by Cagalli in the MBF-02 Strike Rouge.

In Gundam Seed Destiny Phase 39: Kira of the Sky, upon hearing that Lacus and her ship Eternal were under attacked by ZAFT forces, after investigating the remnants of the space colony Mendel for clues about Chairman Dullindal's plans, Kira rushed back to space in Cagalli's Strike Rouge mounted on booster rockets. Being outnumbered and outclassed by ZAFT's Zaku and GOUF squadrons, Andrew Waltfeld told Kira whose Strike Rouge was seriously damaged to go into the Eternal to pick up his new unit. Back in the Eternal, Kira and Lacus were reunited. After some initial hesitations, Lacus finally presented Kira with his new unit, the newly constructed ZGMF-X20A Strike Freedom Gundam. In the first battle, he disabled the ZAFT mobile suits and three Nazca-class destroyers. Kira is last seen providing escort to the Eternal just in case there are more ZAFT attacks. Kira will be rushing back to Earth with Strike Freedom to help Cagalli defend Orb Union which provided shelter for Lord Djibril in addition to delivering ZGMF-X19A Infinite Justice to Athrun Zala.

When Shinn launched in Destiny to confront Cagalli's Akatsuki, just when Shinn's beam boomerangs were about to finish off Akatsuki, Kira appeared from the sky, hand in hand with Infinite Justice (Lacus Clyne was piloting Infinite Justice during re-entry at that moment), Kira fired the rail guns to blow away Shinn's beam boomerangs. Everyone was surprised by the appearance of the new "Freedom" which was supposedly destroyed in phase-34. Kira then engaged Shinn and were evenly matched shot for shot. Kira then went into SEED mode, and when Shinn tried to use the anti-ship sword to slice Strike Freedom, he grabbed and removed Shinn's anti-ship sword and fired the rail guns point-blank range at Destiny, which angered Shinn and made him go into SEED mode as well. Kira and Shinn then exchanged several fly-by beam rifle shots. Having fought a prolonged battle first against Cagalli's Akatsuki and then Kira's Strike Freedom, Destiny's Hyper Capacitor was low on power and was recalled back to the Minerva by Rey to recharge and resupply. With Destiny no longer on the battlefield, Kira then disabled many of the ZAFT mobile suits invading Orb and thus single handedly turned the tide of the battle. When Shinn relaunched accompanied by Rey, Kira in SEED mode managed to hold his own against them. Kira was immediately engaged by Shinn with several fly-by beam rifles shots. Shinn then used Destiny's beam wings to boost speed and got close to Strike Freedom. Shinn tried to fire Destiny's "Palma Fiocina" palm beam cannon to blow up Strike Freedom. However, before Shinn can unleash the palm beam, Kira moved away from the palm's trajectory and then kicked Destiny's arm away. This maneuver caused Destiny to be temporarily disoriented and vulnerable. Strike Freedom took aim at the helpless Destiny, only to be distracted by the Legend at the last moment. Rey then engaged Kira by shooting his DRAGOON funnels attached on Legend's backpack in order to help Shinn set up a kill. The large amount of firepower of the Legend got the Strike Freedom out of balance and was target locked-on by Destiny's long range beam cannon. Shinn was about to fire a possibly damaging blow when suddenly the beam boomerang from the shield of Athrun's Infinite Justice stopped Shinn from firing.

Thereafter Kira faced off against Rey's Legend, while Athrun engaged Shinn in melee combat proving himself superior by hacking off the Destiny's wrist despite his injuries. After the ZAFT forces retreated, Athrun lost consciousness and lost control of Infinite Justice and was falling down. Kira in Strike Freedom caught Infinite Justice in mid-air and prevented a crash. When Kira removed Athrun's helmet and flight suit, Athrun's wounds have re-opened and was bleeding profusely. Kira then ordered a stretcher to bring Athrun to Archangel's sick bay.

When Cagalli's televised broadcast from Orb Union's Parliament was suddenly interrupted by a broadcast by Meer Campbell (Lacus impostor), Kira flew Lacus in Strike Freedom's cockpit to Orb's Parliament in order to retake the broadcast from Meer Campbell.

Following the destruction of several PLANTs, ZAFT withdrew its forces from Orb's coastline, and sent its Flagship the Minerva to reinforce the ZAFT Lunar Team in attempt to destroy the Earth Alliance's Lunar-Based Laser Cannon, "Requiem" (which fired and destroyed those PLANTs). During the time, Archangel was officially commissioned into the Orb Forces, and Kira was promoted to General, and appointed as the commander of the Orb Space Fleet, which is assigned to destroy the "Requiem" and stop Dullindal from accomplishing the "Destiny Plan."

When Archangel returned to space and docked in the lunar city of Copernicus, Kira accompanied Lacus to do some shopping, annoying Athrun. There, they received Meer Campbell's red haro containing a message from Meer requesting to meet with Lacus. When Meer and Lacus finally meet, Sarah (Meer's bodyguard) had organized a team of assassins to kill Kira and Lacus who were accompanied by Athrun and Meyrin Hawke to fight them off. Athrun requests backup from the Archangel which sends Mwu La Fllaga (Neo Lorronke) to aid them in the Akatsuki (ORB-01). Just when they thought it was safe, Sarah who had not died in the explosion resulting from a grenade aimed her gun at Lacus intending to finish her mission at all costs but, Meer who saw her quickly pushed Lacus out of harm's way sacrificing her life. Thus, Athrun quickly disposed of Sarah before she could do any more harm.

In the final few episodes of Gundam Seed Destiny, Kira and Athrun quickly become a major part of the final line of defense between the world and Chairman Dulindall's Destiny Plan. In the final battle, Strike Freedom confronted with Legend in a one-on-one battle.The Strike Freedom managed to destroy several of Legend's DRAGOONs before using the attacking the Legend directly, disabling it. After that, the Strike Freedom docked with a METEOR once again and used its power combined with the Strike Freedom and attacked the inside of the space fortress, Messiah, leading to its eventual destruction.

Then, Kira went to meet Gilbert Dullindal in the command center of Messiah. While they were talking, the captain of the Minerva, Talia Gladys, arrived. Gilbert was shot down by Rey Za Burrel, who had snuck, unnoticed by Kira, into the command center. With this talk, he succeeded into moving Rey, with his desire for a future, something that was denied to him, so he shot Gilbert, instead of Kira. Before leaving the Messiah, Talia Gladys asked Kira to tell Murrue Ramius, the Archangel's captain, that she had a son and she wishes that Murrue Ramius will meet her son someday. Kira was able to leave the Messiah in Strike Freedom before it fell to the moon surface and exploded.

Kira stated that he is prepared to fight to defend the shaky peace and to ensure that humans never again go down the path of all out war. It is likely that Kira is a central figure and a commander of Terminal (Three-Ship-Alliance) and the Orb Military. Kira's accomplishments in both the Bloody Valentine and Junius Seven Wars have definitely proven that he is one of the most skilled mobile suit pilots in the Seed universe.

Kira made peace with Shinn Asuka at the memorial for the fallen, at Orb later (after the war), promising the latter that they would "replant the flowers no matter how many times they would be blown away" and to "fight together".

Kira is finally seen wearing a white ZAFT uniform without specification of his rank or role in ZAFT or whether he is part of Lacus guard. He is seen with the Trooper trio, Shinn, Lunamaria, Meyrin (still in ZAFT) and Athrun (admiral of Orb). He met Lacus before she entered in the council room and they rushed toward each other to embrace, startling many people, though Yzak, Dearka, Shiho, Athrun and Meyrin are smiling

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.

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 handguns, preferring not to use them. He even has to be reminded by Mu to remove the safety on his gun in episode 44 while in pursuit of Rau on Mendel station, Then Gundam Seed Destiny, his handgun skills improve dramatically as seen in the second assassination attempt on Lacus Clyne. He is shown as a skilled unarmed fighter and is extremely effective with his mobile suit's artillery. His suggest status as a person with sensory ability of a Newtype also has an impact on his fighting abilities.

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 has grown mature and has even had some philosophical talks with Athrun and others. He felt down when Lacus went to space without him and even more when he lost the Freedom. He is still quite shy but actually strong minded, but he won't go back on a decision. He doesn't like ZAFT Chairman Durandal since Lacus was targeted and is being impersonated, he doesn't believe the chairman as does Athrun. During the final batle against ZAFT forces, Kira is surprised when the remnant soldiers saluted him and even more so when he saw that it was making Murre smile. They showed to him great respect, with Amagi even calling him Master Kira (Kira-sama). When he gave the order to the Archangel to destroy Requiem, he was unsure : "Um... This is an order". He never had a grudge to Shinn Asuka (despite Shinn destroying Freedom Gundam in revenge for killing his family) and was seemingly happy to meet him. Kira's way of fighting is to disable MS and ships as he doesn't want to kill, which can be a disadvantage in battle. He acknowledged the fact his hands were tainted with blood.