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Super Robot Wars Compact 3 was the last SRW to be released on the WonderSwan line of handhelds, and is the only game in the series that exclusively appears on the Wonderswan Color. While elements of Super Robot Wars F (Game) and F Final remain (the Limit stat, lower HP values, visual style, Londo Bell (Concept) as the protagonist team), Compact 3's gameplay is influenced by Super Robot Wars R (Game), Original Generation, and Alpha 2; the ability to skip battle animations and the ability to purchase pilot skills are two of the many changes introduced. The game has no outer space missions whatsoever; this may be due to the presence of The Vision of Escaflowne. Aside from the debuting series, every anime series included in Compact 3 was featured in the previous Compact games. New Story of Aura Battler Dunbine, which provided bonus units for the Dunbine TV characters in previous games, finally has its story utilized in Compact 3; it, along with The Vision of Escaflowne, is used to create a very fantasy-based setting. Mechander Robo is a 70s Super Robot series, while Betterman is more of a horror series then a proper robot anime.
The Earth was nearing what seemed to be the end of a long, painful war. Dr. Hell, the Mikene Empire, the Hyakki Empire, Neo Zeon, and the Organization of the Zodiac have all been defeated, with the Cambellians and the Titans on the verge of destruction.
However, the Earth Federation cuts back at the very last minute: the Argama is forced to finish off the Titans remnants on its own, while the Super Robot teams are left to deal with the remains of their respective enemies without assistance. Because of this, a half year passes with little-to-no progress being made against completely destroying the various factions.
Little do they know that a new war is about to begin...
A list of the anime series which are featured in the game. Series that premiered in the Super Robot Wars series in this game are marked with "(new)".
End-of-Mission PP System. Based on the player's performance during a mission, extra PP can be distributed to surviving pilots at the end of the scenario.