For completeness, here's a summary of the theory:
50+ years ago on his quest to cure his granddaughter's disease Gerald examines the ruins of the Echidnas on Angel Island. Gerald starts his work by creating creatures based on Perfect Chaos (from the SA1 mural), creating the artificial chaos and the Biolizard. His work culminates in the ultimate lifeform, a blue hedgehog with the ability to control chaos as depicted in the S3&K mural.
GUN, fearing the ultimate lifeform's power invades the ARC, killing Maria, but not before she jettisons the ultimate lifeform to Earth. Gerald is captured, and forced to create a new ultimate lifeform under GUN's control. Gerald creates Shadow, filling him with a mix of his own will and the memories of the original ultimate lifeform as revenge. GUN realizes this and executes him.
40+ years later, the crashed pod opens on Christmas Island, although damage from the crash has caused the ultimate lifeform to lose his memories.