My theory is this; The beast Trio of today were, before death, the ledgendary bird trio. It was said that Lugia(the bird trio master) once roosted in the Burnt tower. Also, the tower was hit by lightning. this may have weakened the trio(due to their shared weakness of electric type attacks) and rendered them unable to escape, or possibly been the cause of death. Though it would have had to have been an extremely powerful attack. Possibly a lightning type Judgment from Arceus himself? if so, for what reason?