To beat the final boss, have an army of all samuris, supported by covering fire (Invasion strategy building) and when you have like 5 guys left, use the Zeus strategy. This brings 60% of your dead samuris back. Also make sure to set them to will, and make them also swarm the boss, by bring their command tab slightly behind him, then clicking hold, then wait intill they get there and click will. If this doesn't work, the next wave of full samuris will :) (P.s. Have all 3 islands next to it be filled with samuris)
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