Gameplay takes place in the Fragmented Sectors, an area of outer space filled with asteroids that are rich in mineral resources.

The player can use the proceeds for empire expansion, purchasing new technologies, construction of buildings, ships and missiles, spying, trading and also to pay fines should the Federation impose any.

There is also a black market offering unauthorised information regarding individual spies and colony supervisors, and illicit trade in rare ores and missiles.

Ships range from the small Scoutship (used to discover new asteroids), to the gigantic Command Cruiser (which is used for transporting combat fleets over vast distances that they would otherwise be unable to travel without refueling).

If a faction is found to be trading with the Mauna, Jane Fong (Federal minister for trade relations in addition to her role as Terran ambassador for the Fragmented Sectors) can be informed, who will in turn tell the Federation, which could result in increased hostility towards the offending faction from all others or, they can be threatened with blackmail and forced to pay a tribute in return for the players silence.

The chances of an agent successfully completing their mission and escaping detection are increased if there is a spy satellite orbiting the asteroid they are assigned to.

There is no research in the game, as this popular mechanic is replaced with the Sci-Tek blueprint system which allows players to buy new technologies as needed.

[6] The player begins the game as the latest recruit to TetraCorp's mining franchise operation and is tasked with selling as much ore as possible to the Federation, which is a coalition of six of the seven known alien cultures: the Terrans, the Artemia, the Mikotaj, the Achean Gatherings, the Braccatia and the Rigellians.

The Federation was inaugurated in 2439 following a coup deposing the last Terran Emperor Dramon Salaria in 2437 and was established to encourage commercial competition rather than full-scale wars between its constituent parties.

The opening cinematic plays like a corporate recruitment video and at one point is interrupted by a Terran male who tells the viewer that TetraCorp has a history of exploiting workers of all races and cultures with low pay and wretched working conditions.

The movie is interrupted a second time by an Artemian who tells the player that Terran progression was responsible for 68% of all alien mortalities during the past three centuries and that the reason for this high percentage is due to megacorporations such as TetraCorp.

Fragile Allegiance is essentially a remake of Gremlin Interactive's 1994 Amiga game K240, with the graphics and user interface revamped for the improved PC hardware available at the time.

The core gameplay elements of K240 are retained; the game is set in an asteroid belt, the Sci-Tek blueprint system replaces research and the player is tasked with building up a successful mining operation.

[10] Fragile Allegiance was marketed as an intense deep space real-time strategy game complete with complex face-to-face diplomacy.