The crew members from Heliopolis get to see their families again. Kira stays behind on the ship though. He and Flay have a spat. She accuses him of pitying her and also during the fight he says that, “It was a mistake” indicating their relationship.
But it’s to Mu that he gives the real reason why he doesn’t want to meet with his parents, “Why did they make me a Coordinator?”
And then Birdy, his robot bird made by Athrun, flies away and out of the hangar. Then Birdy lands on Athrun. Through the fence Athrun and Kira have a small chat pretending they don’t know each other. This confirms of course that the Archangel is still in Orb but Athrun doesn’t say why he’s sure to the rest of his ZAFT comrades.
Their expressions are so heartbreaking though.