The main differences to the original release include:
- Additional weapons: Stones, Iron Lizard, Enemy Chaser, Super Grenade, and Drop Shot.
- Additional power-ups, items, and prisoners in most of the levels.
- Additional times of the day: stages can take place at twilight, sunset, or dusk.
- Some of the locations and vehicles in the game have been altered.
- Increased enemy count. Some of the enemies’ placement has been changed.
- Many weapons have a stronger explosive force. Explosions yield more unexpected results.
- The soundtrack has been re-mixed.
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Some classic weapons from previous also got more powerful versions of themselves with greater firepower, indicated by the pulsing letter of their pickup icon.
Some stages were altered in various ways, such as the time of the day (Mission 1 starts at dawn instead of day, for example), enemy, boss and item placement. Slowdowns that plagued the previous version were minimized greatly thanks to the new placement, and various bugs were fixed in this version. Rearranged item placement also enables the fat transformation to appear early in Mission 3 instead of exclusive on Mission 4. Music and sound effects were remixed and improved for this game.
The announcer from Metal Slug and Metal Slug 2 were replaced with a new voiceover, which adds more sounds bytes regarding the new weapons. This voiceover would endure until Metal Slug Advance.