It's a couple of years since the events of the first game and Jessica - the former advertising executive turned treasure hunter whose exploits formed the story of the first Deep Blue Sea - has disappeared. Her younger sister Melissa receives a worn postcard with a note in Jessica's handwriting written in the secret code that the two sisters invented when they were young. The note tells Melissa to go to Billinger Island, which is where the search for her sister - and her own adventure - begins.

Like the first game, levels in Deep Blue Sea 2 take the form of underwater dives where you'll match various shells and undersea symbols in groups of three or more. There are two goals here: collect valuable treasures by making them fall to the bottom of the screen, and matching coins to fill up a treasure chest before Your breathing tank runs out of air.

Before you go on a dive you can suit up with gear (power-ups) to help you on the playing field, such as tile-breakers that break a single tile, explosives that clear a 3x3 area of tiles, and extra air. You can either choose equipment yourself, or select "Auto Equip" and let the game choose what it thinks are the best power-ups to take alonG.
You'll start out with MelIssa, but eventually new divers will be added to your crew, each with different abilities and skills. For example, some are more savvy at finding treasure than others, while some can conserve more air on a dive. Characters earn experience from diving that increases their abilities even more.