In book 11, Kyon travels forwards in time and impregnates Mikuru's mom, but then as a side effect of abusing time travel he then de-ages eight years and becomes a girl. He then is sent back in time to three years before the events of Haruhi Suzumiya, where he is left at his own house and through creative rewriting of people's memories to try to restore the historical record, he is made into his own sister.
With his old memories quickly fading, Kyon eventually fully becomes "Kyon's sister." As time goes on, Kyon's sister grows up to become a beautiful scientist who invents time travel. But in one of her earliest experiments she accidently summons a young man from the past who she has a sexual relationship with. She has to send that man back to the past, but she has a child of this she names Mikuru.