The player once again jumps into the role of Emerald "Deadeye" Flint. After the Bionts are defeated, Flint goes back to being a mercenary as a leader of a Biont-hunting task-force. Things turn for the worse when his submarine, the Succubus, is stolen on one of the stations. The game begins with one of Flint's dubious acquaintances giving him an old, barely-working sub and several missions to get him started.
Throughout the game, Flint earns money by completing missions, allowing him to purchase better subs, weapons and equipment. The new equipment appears throughout the game, available for purchase, as the player progress in the storyline. Generally speaking, the player is allowed to buy a new boat and a new set of weaponry per chapter. While on stations, Flint can speak with various characters in order to get new missions and deepen the atmosphere of the game.
The former system of upgrading the vessel with a variety of defensive turrets has been simplified by fixing the player's view to the cockpit as well as permitting the usage of only two on hull installed cannons. As the result of this change, the controls of the submarine have been adapted to the first-person shooter's mouse-based layout, removing the need for the joystick, thus the game has compromised its tactical depth in order to increase the insensitivity of combat. This change has raised critique among the reviewers, stating that the developers' focus fell inadequately on the visual performance rather than the actual gameplay of its predecessor. Desslock (2001-11-30). "...But while Archimedean Dynasty was a complex, mission-based simulation with trading and privateering, AquaNox is an arcade-style action game that abandons or greatly simplifies those elements. Combat is fast paced and more similar in style to Quake's, or even a rail shooter's, than it is to the more tactical battles in other underwater sims.".
The game was one of the first applications to fully use the T&L effects by supporting the NVIDIA Geforce 3 Ti graphics accelerator. Desslock (2001-11-30). "Considering the game engine has been used for months to market Nvidia's flagship GeForce 3 video card, it's no surprise that the graphics are outstanding. The game has been designed to take advantage of all the high-end capabilities of the GeForce and its latest generation of cards, and the environments look amazing as a result. Textures are colourful and extremely detailed, and there are numerous little graphical touches, such as chips that flake off underwater hills hit by your projectile weapons."
Aquanox 's difficulty level is clearly above those of other games released in that year. The prime challenge is built by the inability to save in any way during missions, meaning that being destroyed or aborting an objective will result in the restart of the operation. The success of the player during each mission depends strongly on his submarine configuration and weapons aboard.
As the sole member of the series, the game includes a vast amount of true information on oceans, such as origins of different species, their specifics and man's adaptation to submarine life. The game manual consists of two chapters explaining various terms and facts that have been mentioned throughout the course of the story.