立藤美学园,仅仅因为一个入侵者——“它们”,而化作了地狱的坩埚!“它们”袭击人,咬人,产生出新的“它们”席卷了整个学园。在化成恶魔的世界的学园内,小室孝和青梅竹马宫本丽、朋友井豪永,暂时去避难。但是,为了保护丽而被“它们”咬的永却变成了“它们”……剩下来的两人,与其他幸存者,同级同学高城沙耶、平野户田、剑道部主将毒岛冴子、校医鞠川静香汇合,下定决心逃出学园!他们有办法活下来吗!?
“信号塔大战”后,熊大、熊二和光头强的缩小器再度遗失。三人组合继续留守不夜城,找寻缩小器的回家之路更是状况频出,但他们从未放弃希望,最终与小动物们合力拯救小镇,呈现了一场精彩惊险的微观世界冒险之旅。
Some autobots are captured. The remaining Autobots team up with some rebels to free their friends, the rebels know all the weaknesses of their enemies machines. They merge with the Autobots to become Headmasters to free their friends.