Border of Madness does not feature mission rankings or the option to play two scenarios, as the story of Border of Madness was reworked to be more 'linear.' Several weapon classes have also received changes - shotguns now fire multiple rounds per attack and rifles are now purely long-range weapons. Other returning features include armor coating, mission branching, part sorting, and remodeling.

The linked units must also be free to act on their turn, as using Links ends the turns of the involved participants. All weapons can be used for linked actions, however, linked units cannot use the same class of weapon. Up to two units can be linked together to form one 'link'. Links are a unique ability that allows multiple units to provide offensive support to each other during the Player Phase of battle. The most significant of these additions is Links. In 2089: Border of Madness, numerous gameplay mechanics from other Front Mission entries were implemented in the game. Lastly, players can choose to play two unique scenarios - one for the Oceania Cooperative Union, and one for the United States of the New Continent. Mission rankings also make a return based on the scoring system of Front Mission 3, players can earn new parts and wanzers by doing well during missions. Like in Front Mission, players can fight other players to win monetary rewards. Due to its mobile phone format, the story of Front Mission 2089 is told through episodic content with new episodes being released for download on a bi-weekly basis. A returning feature in the game is the Arena.

Missions in Front Mission 2089 are traditional tactical RPG fare, ranging from destroying all enemy targets to protecting a particular allied target. The game progresses in a linear manner: watch cut-scene events, complete missions, set up wanzers during intermissions, and sortie for the next mission. Front Mission 2089 borrows many of the gameplay mechanics present in Front Mission First.

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