Is that Itsuki or Ayato with Haruka in the end?
That’s Ayato! The reason why Ayato looks so much like Itsuki, is because Ayato and Itsuki are actually twin brothers (Ayato still keeping the older brother status). How are they twins you say? Itsuki explained everything to Haruka in one of the later episodes in the series; he said that both him and Ayato are actually clones from the Bahbem Foundation… though they are indeed superior clones to the mass produced ones (the D’s). They were made from genes taken from Quon (while she was in her stasis), and Watari Shirow (who most likely volunteered). The reason Bahbem created them is because previous clones using his own genes weren’t functioning. So he had to fuse a product of somebody purely Mu and a human to make his experiement work or balance out. When Rikudo and Watari found Quon and Maya at the Shrine of Time, it was like hitting the Jackpot, since Bahbem was searching for a Mulian all those thousands of years he was establishing the Bahbem Foundation. When the two boys were born,
