大战结束后——世界的主流不再是军队间在台面上展开的武力冲突，取而代之的是间谍们在暗中行动展开的「影子战争」。在迪恩共和国的间谍培育学校中成绩吊车尾的学生「花园」百合被选拔为执行不可能任务所新设立的团队「灯火」的成员。而等待著前往赴任的百合的，是以「世界最强的间谍」自居的青年：担任老大的克劳斯。以及一群奇特古怪的少女们。

间谍团队「灯火」的训练生活开始了。但是隶属于团队的成员却是一群吊车尾的少女，而且身为老大的克劳斯也完全不是当老师的料。再这样下去她们的第一次任务恐怕会以失败告终，并无可避免地走向全军覆没的结局⋯⋯?

团队「灯火」的第一场任务是「不可能任务」。她们潜入帝国内的军事研究设施，却遭遇出乎意料的伏兵。面对其压倒性的战斗力，少女们被迫面临以命相搏的战斗。

团队「灯火」的第一场任务顺利成功。身为最后王牌的第八名成员・爱尔娜在训练刚开始时迟迟无法融入同伴们的圈子。经过一番烦恼后，她展开了某项大胆的行动。

为了让克劳斯投降，「灯火」的少女们策画了夺取机密文件的计划。擅长偷窃的席薇亚成为了计划执行者，并独自在街道上跟踪克劳斯。

训练期如今也终于进入尾声。而庶民出身、心地温柔的莎拉直到现在都还是对自己缺乏自信。某一天，克劳斯向少女们提出了以宅邸修缮为主题的特殊比赛挑战。

“灯”第一次任务后的休假结束，接到了第二个不可能的任务。但是格蕾特看出克劳斯在暗中积攒疲劳，开始担心他的身体。

为运行杀死暗杀者的任务，克劳斯挑选出了「灯火」中最强的四人。被选上的葛蕾特等人前往某个老政治家的住处，以女仆的身分潜入宅邸ーー 。

袭击宅邸的「疤面男」是帝国派出的暗杀者吗？在众人变得越疑神疑鬼的过程中，葛蕾特和女仆长奥莉维亚之间的对立开始渐渐加深。另一方面，克劳斯也终于亲自展开行动ーー。

奥莉维亚原来是帝国的暗杀者「尸」的搭档。由于无法指望克劳斯前来救援，葛蕾特等四人现在即将面对以命相搏的战斗，她们究竟能否全员生还呢…?

第二项任务「狩猎暗杀者」总算是成功了。在离开任务运行地点、准备返回的半路上，葛蕾特的脑中浮现出某个回忆。那是在运行任务前的休假期间发生的一个小小的事件。

Sometimes, you have to give yourself a little reward to make it all worth it.

Under rare circumstances, cornered spies will turn to desperate acts of violence. All they can do is pray that others don't get dragged into the situation.

The team faces a moral dilemma over Matilda’s fate. She may be an enemy spy, but she is also Annette’s mother.

There’s only one way to get Matilda out of a jam and sneaking her into a cargo freighter leaving the port may be the team’s last hope.

Everyone is starting to slip up and show signs of psychological strain. Everyone, with one exception.

This will be the first time in a long while that all nine Lamplight members back together!

Annette runs out of spending money buying parts for a machine she is building. The solution? She gets a side job!

The latest mission is going to involve infiltrating a foreign country. This will be a major trial for Lamplight.

The group questions bringing Roland with them. Unfortunately, he’s the only one who knows what Purple Ant looks like and that makes him valuable.

Someone once told Miranda that when she was in the depths of despair, a hero would come to save her. Will that be true in practice?

An intense encounter at a bar. Tears are shed. A gun on the table. What is going on here?

All roads have led to this as Lamplight shines in this thrilling season finale of Spy Classroom.