High Seas Havoc includes an anthropomorphic protagonist; many anthropomorphic characters appeared in 1990s video games.

The story is about a pirate seal named Havoc (Lang in the Japanese version), his young sidekick Tide (Land in the Japanese version), a girl named Bridget, and an evil pirate named Bernardo. Bernardo is looking for Emeralda, a gem with powers that can cause whole armies to be toppled. A map shows where Emeralda is located, and Bernardo is looking for the map. Havoc and Tide discover Bridget unconscious at a beach. When she wakes up in a dwelling, she instructs Havoc to keep her and the map safe. Havoc hides the map in a cliff. After Bernardo's henchmen finds Bridget, he kidnaps Bridget and Tide; this causes Havoc, the playable character, to set off to rescue Bridget and Tide.

High Seas Havoc contains some similarities to the popular Sonic the Hedgehog series. These include character appearance, gameplay, and the look and feel of levels.

1. Cape Sealph - Pirate Ship
2. Otarucean
3. Burning Hamlet
4. Mt. Chester
5. Frozen Palace
6. Mt. Bernardo
7. The Final

Each level apart from the first and last have two acts. The Cape Sealph level was removed from the European version.