Few contain the internal docking ports of the prior games, instead featuring external docking clamps. The stations are restructured, larger and more detailed. Graphically, Egosoft redesigned everything from scratch. X3 uses a new, specifically developed graphics engine to give highly detailed renders of ships and stations, along with photo-realistic planets and a host of new effects, including lighting, shadow and reflection. The player is free to go anywhere in the X-Universe at any time and explore, complete plot-related goals or to fulfil their own personal goals. Most ships seen in the game can be bought or captured, and flown by the player. Different ships are available for various tasks: small, fast scouting ships freighters powerful battleships and massive carriers for moving a fleet. The main quest can be postponed or ignored as the player explores the expansive universe and spends the most time in control of a ship, doing tasks of their own choosing.

X3: Reunion incorporates open-ended 'sandbox' gameplay.