In the FMP light novels, the ultimate plan of the Big Bad Leonard Testarossa and the organization he heads, Amalgam, is to
remake the entire world into one more to their liking, along similar lines to other anime villains such as Seele, Madara, etc. To that end they take over Merida Island and install a system built by Kaname.
How exactly were they planning on achieving this?
How exactly Amalgam's technology was supposed to rewrite history and change the world is unclear to me. From what I can make out, it somehow involved time displacement that was related to the Whispereds' abilities (i.e. they were telepathically receiving information from the future).