"Athrun? Something on your mind?"
Athrun looked back from the ocean to see Kira approaching. He turned back to watch the waves kick the shore. Kira sat beside his friend, waiting. If Athrun did not want to talk about it, he would say as much. The fact that Athrun had not said anything yet told Kira that Athrun did want to talk.
"... my father's dying wish." Athrun struggled to keep his voice steady. "I never knew how he truly felt about me after Junius 7, underneath his madness. I—" Athrun took a breath, grateful for Kira's hand on his shoulder. "He was dying in front of me in Jachin Due. He—he asked me to fire GENESIS, for 'our world, our sake.' I think he believed in me, but I don't know—" He shook his head.
Kira silently put an arm around Athrun. So that's what he's been bothered by, ever since the end of the war. To have his father's last wish be something that went against his morals, his goals, just like that...
"I saw it in his eyes again, Kira. I could see that he loved me, that he probably believed I would fire GENESIS for him, but I still don't know what to make of it... I hadn't seen it for so long... I thought he always regarded me as a soldier, and only a soldier, ever since I joined ZAFT. He rarely allowed me to call him 'Father.'" Athrun nearly broke down right there. "I've always wanted to make my father proud, but...!"
Kira could only hug Athrun, who now had tears running down his face. At least he's letting this out instead of bottling it up...
AN:
My writing fails. I know. I'm better with academic essays, not storytelling. xD
I feel that this isn't something that gets a decent amount of focus (if any at all) in fanfics. Athrun loved his father, enough to shed a few tears when the old guy died despite saying he was disappointed with his father to the old guy's face. His father's dying wish (significant since there will never be another chance for dead people to make wishes) must have really hurt... He probably got over it (mostly) by GSD, but still.
Haven't watched GS in a while (school, not to mention I've been considering... uh... broadening my fandom range), so I'm probably off with a few things.
Characterization may or may not be influenced by other fanfics and headcanons.