War for Zeon Independence adds an updated map system and military system to a rewritten script, several new characters, an updated spying system and Mobile Suits from MSV. The battles are fought in full 3D, unlike previous titles in the series. However, this installment omits the Zeta Gundam era conflicts featured in Blood of Zeon. As a result, the Principality of Zeon and the Earth Federation are the only factions featured in this entry. However, after completion of the game with each team, an option to use them in IF mode is unlocked. Each completion of the game increases the player's "IF" Level and more points to use in IF Mode. IF Mode allows the player to create their own team; Choosing such options as a leader (or creating their own leader), Their home base, which officers to start with, which technology group their faction is in and what units the player starts with. This also comes with a variety of Scenarioes to play through, with preset IF modes.

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