Episode 5 has Ayato given a place to stay and Megumi is given the task of showing him around. She is antagonistic towards him at first but warms up as they wait for a rain storm to pass. It ends with her laughing with him when he has trouble with a certain type of drinking glass. Then later her uncle asks him to hang something up: his own sign for the house.
In Episode 24, Haruka admits to Ayato that he was her first love and that she's loved him from afar for more than a decade, not expecting him to return the feelings because his memory had been erased. Instead Ayato tells her, "I may not remember the past, but I know the present. And the one I love is the current you", takes her in his arms and kisses Haruka as she sobs tears of joy. Gets you right in the old heart strings.
Certain endings have Ayato use the godlike Raxephon's power to turn back time to before Tokyo Jupiter came to be and undoing all the tragedy that resulted from it, subsequently allowing everyone to live normal lives as they should have.