Baboo is Dr. Jones's assistant who seems to be hiding something about the recent abduction.

Chief Coralcola is the leader of Coralcola on C-Island. A close friend of Dr. Jones, he delivers the news of Dr. J's abduction and sends Mike on a rescue mission. He provides Mike with his starting weapon, the Island Yoyo.

The Shaman of Coralcola and the Chief's sister. She warns Mike of the dangers ahead but assures him that the magic of the Southern Cross is always on his side. She appears on the Game Over screen to keep Mike from losing hope.

Michael Jones, known to his friends as Mike, is the hero of this story. A 15-year-old honor student and baseball team captain from Seattle, Washington, he travels to C-Island to visit his Uncle Steve, only to find him abducted. Armed with an Island Yoyo and an unyielding spirit, Mike sets out across the South Seas in search of his uncle.

Nav-Com is the onboard computer of Dr. Jones's submarine, Sub-C. Nav-Com ferries Mike from island to island across the South Seas and provides guidance along the way.