Based on "Gale of Darkness"
Even after Lugia has control of full control of herself, her shadow countpart is still here. In her mind. Haunting her. She often hallucinates the Shadow Lugia where ever she goes. Nomatter how many times her trainer takes to the Pokemon Center, the doctors couldn`t find any cure. All she could do sit there, cry in fear and pain, as she hallucinates her shadow counterpart taunting her every single day.

Lugia by Game Freak