In the arcade flight model, the joystick is configured as in a typical space combat simulation, with the stick controlling pitch and yaw and the twist axis controlling roll. In the standard flight model, the joystick is configured as in a high-end airplane simulation. The stick controls pitch and roll, while the rudder pedals or twist axis controls yaw. At any time, in any flight model, you can swap the roll and yaw inputs by pressing the "J" key.

Under normal circumstances, the mouse is used to control the user interface and to manipulate the interactive HUD. When using the third-person exterior view, the mouse is also used to control the camera and to select targets and issue orders to allies, just as in a space-based RTS game. You can right-click on any friendly unit in the chain of command to access a context-sensitive orders menu.

You can also use the mouse to fly your ship and fire your weapons. By pressing the "~" key, you toggle the mouse between selection mode and flight mode. In flight mode, the mouse works much like the "mouselook" control in an FPS game. You steer the ship by moving the mouse in the direction you want to go. Fire guns with the left button and missiles with the right button. Tap the middle button to select a target, and use the mouse wheel to control your speed.

If you prefer, you can also configure the mouse to work as a "virtual joystick." In this mode, the distance of the mouse cursor from the center of the screen controls how fast your ship will turn, instead of how far it will turn. Some people may prefer the "virtual joystick" mode for dogfighting because it requires less repositioning of the mouse than the "mouselook" mode.