Links is a feature that allows multiple units to provide offensive and defensive support to each other during battles.

A unit's AP amount and recharge value depends on its pilot's proficiency levels the higher it is, the greater the amount of AP that can be used and replenished. At the end of a full turn, which is one Player Phase and Enemy Phase, a set amount of AP is replenished. Actions such as moving and attacking require a certain amount of AP to use. Action Points (AP) is a feature that dictates how much actions can be done with each unit. There are a number of returning features from Front Mission 2 that are used for mission play, namely Action Points (AP) and Links.

Missions in Scars of the War are traditional tactical RPG fare, ranging from destroying all enemy targets to protecting a certain allied target. Military bases and supply camps act as intermission points where the player can organize and set up their units for the upcoming mission. The game progresses in a linear manner: watch cut-scene events, complete missions, set up their wanzers during intermissions, and sortie for the next mission. Front Mission 5: Scars of the War borrows much of the core gameplay mechanics found in Front Mission 2, as well as a plethora of features from other Front Mission entries.

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