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So I just finished missile ending of Contra Hard Corps and I realized something about the boss (this thing◊): those faces seems pretty human, even the one in the second part that shoots worms at you. That's when I remember the other ending where you fight colonel when he fused with the alien. The alien cell ended up overtaking him and mutating him to gigantic size. That's when realization hit: Colonel must've shoved some of his men into the missile with the alien cell!