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Lyra was always alone. She just made Khoury up as an imaginary friend, so she wouldn't feel alone. Khoury's father is either Lyra's father, or Khoury's father - Khoury having once existed, but died- and asks the twerps to play along so as not to upset Lyra. And anyone who browses /vp/ knows that Lyra's a freaking psycho deep down.
She had the Totodile and Gible. Any scenes of the two being apart are actually Lyra's imagination - she's either being Khoury or Lyra, or the events of the episode were altered from what originally happened to fit her own personal canon.
tl;dr: Khoury was created to help Lyra cope with lonliness or something.
Or because they wanted someone to have a Totodile, since Lyra and Dawn had the other two Johto starters.
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