Pressing the joystick downwards while standing will cause the character to lie down on his stomach, allowing him to avoid enemy fire and shoot low targets. The player can also shoot in any of eight directions, including downwards, while jumping. During side view stages, the player can shoot leftward, rightward or upward while standing, as well as horizontally and diagonally while running. The joystick controls not only the player's movement while running and jumping, but also his aiming.

When one of the protagonists jumps, he curls into a somersault instead of doing a conventional jump like in other games. The controls consists of an eight-way joystick and two action buttons for shooting (left) and jumping (right).

Up to two people can play simultaneously, with one player as Bill (the blond-haired commando wearing a white tank top and blue bandana), and the other player as Lance (the shirtless dark-haired commando with a red bandana). Contra employs a variety of playing perspectives, which include a standard side view, a pseudo-3D view (in which the player proceeds by shooting and moving towards the background, in addition to left or right) and a fixed screen format (in which the player has their gun aimed upwards by default).

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