Only one image is displayed on every stage clear, which features Bill Rizer in military uniform carrying a large gun in front of a tan background containing some text.A 2-player game will always be played from the first stage and cannot be continued from higher stages (with the exception of Continues).

The second player must also have a copy of the game to play. Due to system limitations, a 2-player game is only possible via a Game Boy Advance Link Cable.Additionally, passwords exist that allow to start between stages 2 to 6 with 99 lives. A Continue Game option was added, which utilizes a password feature allowing a player to start on any of the five stages after the first stage.This version only has two difficulty levels: Novice and Normal, with Novice mode cutting the game's length at the end of Stage 4.The music from these removed top-view stages, however, was retained and play in their respective stages. The top-view stages ( Stage 2 and 5) from the original Super NES game were replaced with two stages from Contra: Hard Corps ( Military Train and Big Battle).

The player can now lock their character's aim like in Contra: Shattered Soldier, allowing them to move anywhere while shooting at one direction.When picking up a weapon, the player's previously held weapon will drop, allowing them to pick it up again if desired.Bombs and the ability to carry two weapons were removed.Most are gameplay-wise due to the Game Boy Advance's lack of X and Y buttons. The designers made changes to many of the game's features from the original game. This Game Boy Advance version was later released on the Wii U Virtual Console in 2015/2016 in all regions. Unlike the original Super NES game and the previous Game Boy adaptation, Contra Advance was released in Europe and Australia under the ' Contra' name without the ' Probotector' title and robotic characters.

After Contra: The Alien Wars for the Game Boy, Konami released a second portable version of Contra III in 2002 for the Game Boy Advance titled Contra Advance: The Alien Wars EX (released in Japan as Contra: Hard Spirits).

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