The research team's results were sent back to Earth on the "Galaxy space capsule", which malfunctioned, crashed into the ocean, and broke into many pieces.

In both campaigns, the player must complete sixteen levels, called Sectors, which are distributed across five Zones:[4] Dragon Reef, Fossil Trench, Limestone Ridge, Sea Forest, and Hammerhead.

In each Sector, the player's goal is to navigate a submarine (the Neptune) through maze-like passages, collect every data capsule, and reach the supply station at the end.

The box cover illustration rendered by Marc Ericksen depicts the Neptune submarine recovery vehicle hovering above the basin of Fossil Trench recovering glowing toxic data capsules.

Along the way the player will encounter various aggressive and/or territorial sea creatures, which usually move about the level and perform actions in predictable and repeating patterns, as well as non-living hazards like sharp rocks and undersea volcanoes.

The Neptune is capable of firing ink pellets to stun sea creatures and render them harmless to touch, in the manner of an octopus or squid.

Furthermore, the ink pellets are fired in a straight line from the nose of the Neptune, so the player must carefully aim their shots at their intended targets.

The math challenge takes the form of a word problem, and it is up to the player to determine the order of operations involved and arrive at the correct solution.

In the Expert Game, hazards are placed in more dangerous arrangements, the enemies move in trickier patterns and have new attacks, and some screens feature strong ocean currents which push and pull the Neptune in unexpected and undesirable ways.

In the Voyager Game, the Final Sector features four slow but large sea creatures which destroy the Neptune in a single hit; ink pellets are completely ineffective against them.