Second Evolution picks up 20 years after the events of the original game. In that time, Ronyx J. Kenny, one of the characters from the original, has been promoted to admiral, and has had a child: Claude. Claude is the lead character of this story, and at the beginning of the game we learn that he has just become an Ensign in the Earth Federation, and he has received his first mission. His Father tags along to supervise, but doesn't end up doing a decent job of it. As the pair explore a cave during their mission, they stumble upon a mysterious looking machine. Claude wanders off to examine it against his Father's orders, and it ends up teleporting him to a totally different world.
