From the Super Mario Wiki
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Spirit is a statistic in Mario & Luigi: Superstar Saga + Bowser's Minions and Mario & Luigi: Bowser's Inside Story + Bowser Jr.'s Journey, which are both exclusive to the Minion Quest: The Search for Bowser and Bowser Jr.'s Journey modes. It determines the frequency of a trooper's Special Skill activating. The stat can be increased by leveling up minions or using a Spirit Bean, and can also be temporarily increased with the Rally command.