Kira then finds Flay by his bedside remembering the last thing he seen a mech covered in golden armor " Yuto " and tries to get up but is stopped by Flay " its fine Yuto is right here ". Flay then moves aside showing Kira his friend's inert form. A oxygen mask is seen covering his face and a IV connected to his arm. As he recovers, Kira's wracked with grief as he realizes that he let everyone down and let them get killed. Noticing Kira's vulnerability, Flay takes advantage of him and sleeps with him during the night. When Kira's called back into action, his methods are much more brutal all of it being played by Flay.
Yuto awoke to a steady beeping sound as he looked around the room scanning his surroundings. ( " where am i , what happened ? " ) he asked himself not remembering what had transpired in the battle just hours ago. The room he is in is very clean and hospital like, and sees a IV to the right with some monitoring equipment. Yuto closes his eyes and tries to recall what had happened or the last thing he can remember.
Yuto was fighting a battle with Athrun unwilling to let Kira go into battle alone and attempted to save him from falling the last thing he remembered was calling out his name. " Kira " he calls out loud. alerting one of Kira's friends Sai Argyle who runs into the room.
The first thing he said was Kira and asking where is he. Sai then tells Yuto of a battle that occurred just a while ago and again were successful at repelling the attack, he then tells Yuto " one thing concerns me Kira is acting different after the battle Kira used force on me and Flay seems obsessed with Kira as well as sleeping with him, the doctor also told us that your genes are also different and very much like Kira. "
This gets Yuto's attention and he tries getting up and is seen in a lot of pain as he does so. Sai then tells Yuto " no you should rest "
Yuto then ignores it pushing Sai away and gets up walking out of the med bay thinking ( " that creep who does she think she is using and taking advantage of my best friend. " )
Yuto then breaks into Kira's room and sees his close friend with Flay , without another word he walks up to her grabbing her arm and slams her into the back wall, a certain fury can be seen in his icy blue eyes. " FLAY, you dirty creep stay away from Kira. "
Kira is shocked to see Yuto standing and attempts to end the hostility between Yuto and Flay.
Yuto responds " Don't you get it Kira , you are my friend and i don't like to see you being used " Yuto was about to just knock Flay out but Kira catches Yuto's hand stopping him. Yuto then throws Kira off him and storms out the door.
Yuto then holds a fist and punches a nearby wall putting a small dent in it remembering the last thing that Sai said " so I too am a coordinator. "
Sometime later a squadron of ZAFT's TMF/A-802 BuCUE's under the command of Andrew destroy the town of Tassil, Cagalli and other members of the Desert Dawn recklessly chase after them. Several resistance fighters, including Cagalli's friend Ahmed El Fasi, are killed, though Kira arrives in time to save Cagalli. Later, the two of them are sent to gather supplies. As Kira and Cagalli sit down for lunch, they meet a (poorly but effectively) disguised Andrew Waltfeld. Blue Cosmos terrorists attack, targeting Andrew. In the confusion, Kira saves Andrew from being shot in the back. Andrew thanks Kira, and he sheds the disguise, Cagalli realizes who he really is. Andrew's girlfriend Aisha takes Cagalli to get cleaned, When Cagalli confronts Andrew, he pulls out a gun and asks Kira if a war will end when all of your enemies are destroyed. Andrew says he does not know why Kira is fighting his own kind, but as long as Kira pilots the Strike, they are enemies. He then puts the gun away stating that his home is not a battlefield and that Kira had saved him. Because of that, he lets Kira and Cagalli leave. Because they know each other, Kira and Andrew find it difficult to fight in the next battle, where Andrew pilots the new TMF/A-803 LaGOWE to face Kira personally. Kira asks Andrew to stop because the battle is over, but Andrew is determined to keep fighting until one of them is dead. Kira activates his SEED abilities and destroys the LaGOWE that Andrew is piloting. Kira cries after the LaGOWE explodes because he did not want to kill Andrew.
While traveling on the Indian Ocean, Kira remembers his final battle with Andrew, the death of Flay's father, and the destroyed civilian shuttle and begins to cry. Yuto walks up with him while Cagalli hugs him when they both see him. " it's ok to cry, but no more tears alright ? me must be strong to end this war and bring peace across all worlds. "
Cagalli then asks Kira why he was with the the Earth Alliance when he is a Coordinator, a question he herd many times.
Later, when the Archangel is undergoing repairs at Orb, Yuto gos to Kira telling him " sorry about before I care for you Kira , you are like a brother to me I should had found another way to do it but i became enraged when i herd it from your friend. Kira your relationship with Flay is a mistake listen to what your heart is telling you and maybe one day you find the person you love. "
Kira soon ends his relationship with Flay after hearing Yuto's words believing it to be a mistake or she was indeed using him as Yuto stated before. Kira then creates a new OS for naturals to pilot for Orb's MBF-M1 M1 Astray. He also meets Athrun face to face, who is spying to see if the Archangel is in Orb. Although Athrun knows Kira is the Strike pilot, he does not reveal this to the others in his ZAFT team. Before he leaves Orb with the Archangel, Cagalli shows Kira that his parents are watching him depart. Kira asks Cagalli to apologize to them for him, explaining he cannot see them right now, especially when he might say things that he may regret. Kira tells her to be safe and thanks her. As he turns to go inside the Archangel, Cagalli embraces him and tells him not to die and to come back to see her again, which Kira promises.