Devoted to her family’s rice-cake–making business and the high school baton club, Tamako is a little slow when it comes to love. She’s oblivious to her childhood friend Mochizo’s affections, even though all their friends know. With graduation closing in and Mochizo leaving for Tokyo, will Tamako realise her feelings and tell him in time?

“闇之书事件”（参照魔法少女奈叶A's）的10年后。踏入19歳的高町奈叶、菲特·T·哈洛温、八神疾风三人，怀抱着彼此的友情牵绊、为了追求各自的梦想实现而加入时空管理局，并以一流魔导师的身分活跃。
在此当中，出现了新发现的太古遗产“圣遗晶石”（レリック），以及以此为目标而出现的谜样机械兵器“共鸣拓发者”（ガジェットドローン）。为了迅速对应日后被称为“圣遗晶石事件”的状况，八神疾风考虑到设置能够迅速对应的独立部队的必要性，设立了专责处理与太古遗产关连任务的特殊部队——“机动六课”。
另一边，时间回溯到四年前。昴·中岛在遭到机场火灾卷入而几乎丧命之际，由于奈叶的出现而得救。因为憧憬著如同“自己理想中的形象”一般的奈叶，昴在当晚的满天星空之下，做出了“成为管理局的魔导师”的决定。
四年后，经过一番波折而顺利成为管理局的新进魔导师的昴，与训练校时代的伙伴蒂雅娜·兰斯特共同挑战魔导师的升格试验。于远处凝视著两人考试的，分别是认定两人将成为“机动六课”的明日之星而投以注意的疾风与菲特、还有奈叶。在三人的注视之中，随着宣告试验开始的ReinForce II（统御之力zwei）的声音，拉开了“StrikerS”故事的序幕。

凯特（富坂晶 配音）出生于富贵之家，贵为千金大小姐的她身上有着一种天然的领袖气质，能做到临危不乱。罗丝（辻步美 配音）沉默寡言，性格内向，沉静的外表之下隐藏了一颗睿智的心灵。蕾切尔（新谷良子 配音）奔放热情，身手矫捷。克莱尔（泽城美雪 配音）个性强硬，喜欢独来独往。四人均就读于同一所学校。
某日，一场意外夺走了她们共同的好友莉兹（福圆美里 配音）的生命，从灾难中脱险惊魂未定的姑娘们还来不及发现，她们的身体发生了某些诡异的变化。入夜，在神秘蝴蝶的带领下，四人来到了仓库街，在那里，她们邂逅了教官劳拉（田中理惠 配音），劳拉告诉一行人，她们早已经死去，为了继续存活在这个世界里，四个女孩要付出相应的代价。

Cecily's a blushing knight in shining armor. Unfortunately, it seems most battles end with her as the damsel in distress. Her lack of skill and distaste for violence make her an unlikely heroine - until the brooding blacksmith Luke comes to her aid, using his powerful magic to forge blades of supernatural strength. Cecily wields this sacred steel and charges forth to face a dangerous new threat. A cloaked fiend is unleashing demons upon the land, and though he lurks in shadows, the villain is much closer than Cecily can imagine.

Shinkurou Kurenai is a 16-year-old student by day and a dispute mediator by night. Despite his unimposing appearance, he is a strong martial artist, who also possesses a strange power.

While taking various jobs for his employer one assignment leads Shinkurou to live with Murasaki Kuhouin as her bodyguard. Murasaki is the seven-year-old daughter of a wealthy family, who escaped from her home under strange circumstances.