Kira first appears in around Phase-06 of Gundam SEED Destiny. He is staying with Lacus at Markio's place on Onogoro island (the same location as the five-minute OVA Between the Stars) with all the orphans. He is very quiet, and one night he looks to the sky and notices something falling: pieces of Junius-7's ruins. Markio's house is destroyed while they take shelter.
He is a bit unsure of what's happening and what to do about it for the next few episodes. But then in Phase-13, there is an assassination attempt on Lacus herself, and that opens up his eyes - his real role in GSD begins from there. In order to protect her, he convinces her to give him the key to the Freedom Gundam, and from then on he plays a big role in Destiny.
Kira once again aligns himself with the Archangel (commanded, again, by Murrue). He has a significant battle with Shinn Asuka in Phase-34 and is defeated and almost killed, totalling the Freedom Gundam permanently. He then spends some time suit-less on the AA, until he hears that the Eternal (and Lacus) is in trouble, and borrows Strike Rouge to save them. There, he is reunited with Lacus, who gives him the Strike Freedom Gundam (which sports the DRAGOON system, like Providence in the first series).
Though he's definitely not the kid from the early SEED episodes anymore, throughout GSD he seems to lighten up from the seemingly-emotionless person he was in the beginning. In Phase-39 he looks and seems genuinely happy, something we'd not seen from him in a very long time.
Kira was not originally intended to be a main character in GSD at all, but he ended up being one anyway due to his strangely immense popularity. He participates in the final battle with Shinn and Rey, and in the Final Phase + episode, he and Shinn reconcile their differences and shake hands. Aww. ♥