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

Bananette is the daughter of Chief Miracola. She has been spelled into a deep sleep. The only thing that can wake her is the magic scroll from the mountain hermit.

Bate is a young boy living in Tunacola who gives Mike a tip about where to sail next. Without speaking to him, Mike will wander the ocean indefinitely.

Chief Bellcola is the leader of Bellcola. He tells Mike where to find information on re-opening the strait so he can pass through.

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.

Chief Miracola is the leader of the village of Miracola. His daughter has been cursed with a sleeping spell, and he sends Mike on a quest for an awakening scroll — promising to repair the shipwrecked Sub-C in return.

The son of the Mother Dolphin, stolen and in need of rescue. Can Mike bring him safely home?

Dr. Steve Jones, affectionately known as "Dr. J", is Mike's uncle and a renowned archaeologist who set up his laboratory on C-Island. He uses his personal submarine, Sub-C, to search for lost ruins and artifacts across the islands. He goes missing shortly after finding a big rock in some ruins.

Mike goes to seek help in getting into Shecola Castle, but the Fortune Teller can't help him without her Crystal Ball. She dropped it into the pond at Ghost Village, so Mike has to go find it and bring it back to her.

Hook is the fishing master. He teaches Mike the ABC's of fishing before sending him off with a fresh worm.

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.

Mica is a princess and daughter of Hirocon, the Argonian leader. She and a group of children are the last survivors of the planet Argonia — placed inside the time-frozen Three Magic Cubes twenty years ago, just before their world was destroyed. Their rescue is the culmination of Mike's long journey across the South Seas.

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.

This poor Dolphin Mother has had her child stolen! Mike willingly accepts the task of retrieving her son.

After battling to the top of the Mountain, Mike meets the Mountain Hermit. He gives Mike the Scroll of Obob to wake Banette, then Mike runs back to the village with it.

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.

Peter the Parrot is the descendant of Captain Bell's Parrot. Passed down from parrot to parrot was Captain Bell's song to gain access to the organ room's secret. He'll only sing the song if Mike can offer him the gift of a Fresh Worm.

Po is an eccentric poet and hermit who lives near the mountain. He is best known for reciting "Po's Poem", a crucial hint that describes the path needed to reach the top.

Queen Shecola is the ruler of Shecola Island who never leaves her castle, leading the men outside to rumor that she is very beautiful. Mike must venture into the island dungeons to help her, and in return she helps him reach the Mountain and rewards him with a new weapon: the Shooting Star.

This massive whale swallows both Mike and Sub-C whole! Inside, Mike discovers that Baboo has already been eaten as well. To escape, Mike must light a fire — which makes the whale cough him right back out.

Zoda, the Prime Invader, is a ruthless alien warlord who invaded the Argonian home planet and destroyed most of their society. He came to C-Island in search of the Three Magic Cubes that would allow him to wipe out the entire Argonian race once and for all. He kidnapped Dr. Jones to aid in locating them, and will stop at nothing until they are his.