The game has two basic components. The first requires the player to engage in Risk-like strategic decision-making with the goal of conquering the given land mass. The player raises cyborg armies to accomplish this goal. During the second basic component of the game, the top-down battle mode, players can choose to assume manual control of one cyborg in their army during offensive or defensive battle sessions, or let the computer simulate the battle behind the scenes to much more predictable outcomes. This allows players to play only the risk-style board game component of the game. The opposite, battles only, is also possible. Cyber Empires innovated by mixing strategy with arcade action on a global scale.

The game offers a total of nine different cyborgs from which the user can create an army of up to 10 units, that is no more 10 units may occupy one country. The units range from the small fast mercury capable of little damage but a high speed, to the Titan which is the ultimate cyborg capable of long range missile attacks and short range auto-cannon attacks.

The strategy part of the game allows the user to place capitols in any countries occupied by their troops. Countries with capitols in them create extra revenue every turn and can be built upon. The buildings includes fortifications, factories and factory upgrades. Fortifications comes in 3 varieties: light, medium and heavy, but can only protect a country if at least one cyborg is present. Factories come in 3 varieties also, they can have 1, 2 or 4 bays. The number of bays a factory is determined the number of cyborgs it can build at once. The upgrade level of a factory, on the other hand, determines how fast an individual cyborg can be built.

In the games, the player takes up the role of a captain (also called commodore in some translations) and manages a seagoing fleet to participate in trades, privateering, treasure hunting, exploration, and plain piracy.

There are several versions of the game, and it has now expanded to a MMORPG game, Uncharted Waters Online.

SC2 added a large number of species and ship types to the already diverse cast and replaced the first game's strategy-based scenarios with a story-driven space exploration adventure game that included diplomacy with the inhabitants of the galaxy, some resource gathering sub-sections, and instances of the mêlée combat of the first game whenever diplomacy failed.

Interaction with the various alien species is a chief part of the adventure game; the backstory of both the species from the first games and new ones were fleshed out considerably. There are literally hours of dialogue, each species bringing out their characteristic conversational quirks, music, and even display fonts. A two-player mode is available, named Super Mêlée, consisting solely of the ship-to-ship combat. All ships from the first game are available, even if they made no appearance in the story, along with a number of new ones.

The plot significantly impacts the game experience by requiring the player to explore every corner of the galaxy and make discoveries and connections independently.