U-Incorporated 2nd Class Type Unit
Well maybe the villains try baiting them into a trap using the students, but after surviving/defeating the ambush the heroes find clues at the ambush point.
Or maybe some hero recognizes something about one of the attacking villains, it could be player-controlled or one of the many npc goons who were helping. They could then track the recognized villains to base through some good old sleuthing.
Given how much stuff makes up Maki-Mak's attire, this turned out pretty awesome.