My fanfiction stars the legendaries quite alot. Latios and Latias were the original Gods of the Pocket Monster era. Once Latias was killed though by the betrayl of the humans and by the hands of Deoxys, Latios created synthetic Gods which are all the existing legendaries. However 3 of the Legendaries felt a deep connection with the heroes of the story and began to realise Latios' intentions. Basically all the legendaries are evil exept those 3 (Kyogre, Groudon and Suicine) of and Entei, the wise one.