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It attempts to retain as many of the sprites, tiles and other stage content of the original without enough focus on proper gameplay. The Final Score image was also changed into the aforementioned Stage Clear image and features a Rank stats screen based on the player's high score and remaining lives (difficulty and if passwords were used may also affect Rank).Contra Advance: The Alien Wars Ex is a simplified translation of its source material, suffering from inconsistencies and lack of play-testing.
The ending images have been altered to display only imagery from this port of the game. 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.