故事发生在《星战前传：魅影危机》后的第10年，此时银河系正处于一片混乱和动荡之中。在变节的杜库伯爵（克里斯托弗·李）策动下，有几千个太阳星系决定一起脱离银河系共和国独立，然而银河系共和国还不具备足够的军事实力来镇压这些分离主义份子，在武力不足的状况下，银河系共和国联合议会决定组成临时军队攻打分离主义份子，而其中的一名议员，也就是纳波星球前任女王阿米达拉（娜塔莉·波特曼）却力排众意，极力反对这种以暴力对抗暴力的策略，因为这会引发银河系内大规模的争斗和屠戮，但并不是每个人都同意阿米达拉维护和平的决心，于是不断有人密谋刺杀阿米达拉，以达到自己不可告人的目的。
此时已经升任为绝地大师的欧比旺（伊万·麦格雷戈）派出他的徒弟安纳金·天行者（海登·克里斯滕森），负责保护阿米达拉的安全。在《星战前传》里还是十来岁小男孩的安纳金，此时已成长成英俊挺拔、身手不凡的少年。在护送阿米达拉前往安全避难所的路途，一种青涩而微妙的感情开始在两个年轻人心里滋生，这种感情无疑将会动摇阿米达拉一向以天下为己任的处事态度，也将会挑战安纳金作为绝地武士，而必须恪遵的“无怒、无憎、无情”的不二誓言……
与此同时，为了彻查星际冲突的根源，欧比旺冒着生命危险深入到遥远的海底世界，他发现，这个一向被认为是蛮荒之地的区域已被人秘密开发，无数的克隆人试验正在紧锣密鼓地实行，这一切甚至可能影响银河共和国的未来命运，星际战争已经箭在弦上，一触即发……
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