Deadly Tide is a pre-rendered shooter in which the player gets to control a deadly new undersea vehicle. The basic plot behind the game is that the aliens have arrived on Earth, and they are not friendly. They take up residence in the oceans of Earth, and begin to launch attacks on shipping. Plus, they are also slowly raising the level of the oceans, trying to flood humans from the planet. Your mission is to stop them.

The game is split up into a number of stages, taking place in various locations, the ultimate aim being to make your way through to the end of that level in once piece. There are many cutscenes that advance the story.

In the year 2445, a race of hostile aquatic aliens arrives on Earth. One of their ships sits at the bottom of the Pacific Ocean, raising sea levels continuously for 5 years until almost 88% of the surface is submerged. In order to effectively fight the aliens, the fictional Earth Ocean Alliance develops the "Hydras", one-man submarine fighter craft.

The player takes on the role of the last remaining fighter pilot. The objective is to travel through the alien-infested seas and fend off the targets long enough to complete the missions.