Deep Fighter is an arcade submarine simulator with first-person shooter elements. The player takes on the role of a security force officer who has just graduated from college and entered the service. As the story progresses, he rises in rank and gains access to 6 different bathyscaphes. The campaign consists of military and peaceful missions. In between missions, the user is shown briefings. The gameplay is linear. The gamer participates in various operations (there are about 50 of them in total), repairs his bathyscaphe at the docks, opens and installs new upgrades on it. Various weapons are also unlocked for the user. After completing the tasks (they can be completed only in one way, previously invented by the developers), the user is allowed to explore the location in detail before moving the story further.

Deep Fighter can be called the spiritual successor to Archimedean Dynasty and Sub Culture. Events take place in the future, where people moved to live on the ocean floor due to an environmental disaster that occurred on the surface. They built underwater cities and began traveling between them in submarines. However, people had to face several problems: aggressive pirates, sea spiders and a high-tech race of humanoids. Scientists and engineers are trying to build a giant ship, the Leviathan, to take the inhabitants to a safer place. Meanwhile, the protagonist defends the colony.