1945年，游学归来的刑侦专家程慈航（乔振宇饰演），在码头遭遇险情，多方势力为争夺一只铁箱大开杀戒。这只铁箱里，存放着日军细菌武器的绝密档案。警察厅厅长莫采石（巫刚饰演）将铁箱存放在档案馆密室内。由于内奸刘阿常（马仑饰演）的出卖，档案被盗，案情从此扑朔迷离。程慈航获悉此案事关日军细菌武器，向“叔叔”莫采石请战，总署刑侦警察局局长霍然随即特聘程慈航为布衣侦探。程慈航上任后，很快找到蛛丝马迹，顺藤摸瓜接连捕获重大线索，然而他却处处受阻。程慈航既要面对刑侦处处长严达庆（王品一饰演）的百般阻挠，又要揣测莫采石的讳深莫测，还要与他的老同学、对绝密档案觎觊已久的哈金斯斗智斗勇，更要与日本间谍博弈较量。内贼刘阿常的死，留下关键线索，矛头直指莫采石。恋人杨玉琼的牺牲，使程慈航爱恨交加，更加坚定信念一查到底。程慈航最终摧毁档案，大义锄奸，与莫采石同归于尽
晓大义莫厅长自尽审战犯正义得伸张
莫采石怎么也想不到自己日夜守护的五九档案会不翼而飞。当莫采石从哈金斯那里回到警察厅，打开保险柜不见了五九档案，他惊恐万分。 这时，程慈航打电话要见他，莫采石看到程慈航手中赫然拿着那个装着五九档案的铁匣子。程慈航指责因为莫采石的愚忠，隐瞒了五九档案，造成许许多多无辜的人为此失去生命，特别是欧阳倩寻找…
藏经阁大有秘密莫采石原是主使
警员告诉程慈航，尸检显示刘阿常是酒后失足溺水身亡。程慈航发现刘阿常手中紧紧攥着一个玉佛。刘阿常的被杀，似一道闪电把程慈航心照得通亮，又被撕得隐隐作痛，他已经可以把事情的始末完整地还原出来，但还缺乏五九档案的下落。 程慈航不知道刘阿常握着这个玉佛到底想说明什么，他在刘阿常家中发现《妙法莲华经》中藏着…
莫采石杀人灭口刘阿常失足溺亡
吃了哑巴亏的哈金斯找莫采石兴师问罪。莫采石告诉哈金斯，严达庆勾结江湖人士，已经被警察厅开除。 欧阳倩的牺牲给程慈航重重一击，霍蜜儿也不知道该如何安慰程慈航。程慈航整日借酒浇愁，已经把程慈航当做兄弟的刘阿常精心照顾他。程慈航认为是自己的固执害了欧阳倩，自己罪孽深重。刘阿常告诉程慈航，自己早就知道五九…
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