Whether he was orphaned or abandoned, he doesn't know, but it doesn't matter anymore. Mallys was raised alongside his (adopted) brothers until the death of their father figure drove them apart. After nearly 600 years of growing up a wanderer, Mallys finds friends which sends his life in a new direction. He's latched on to Arceus (the reverse is also true) and has slowly become good friends with Mel after they've worked past their differences.
