Based on Philip Pullman's third book The Amber Spyglass, the third season is the series last. 

The rebellion against the Authority becomes open warfare, with Asriel working to build a new Republic of Heaven. But to achieve his ends he needs the Subtle Knife, which is currently in Will's hands.

Lord Asriel has opened a bridge to a new world, and, distraught over the death of her best friend, Lyra follows Asriel into the unknown. In a strange and mysterious abandoned city she meets Will, a boy from our world who is also running from a troubled past. Lyra and Will learn their destinies are tied to reuniting Will with his father but find their path is constantly thwarted as a war begins to brew around them. Meanwhile, Mrs. Coulter searches for Lyra, determined to bring her home by any means necessary.

女主角莱拉·贝拉奎亚成长于英国牛津的约旦学院。

在她前往伦敦寻找失踪的朋友罗杰的过程中，莱拉发现一系列儿童失踪事件与神秘物质尘埃有所关联。

随着故事展开，她还发现了涉及到阿斯瑞尔勋爵和玛莉莎·库尔特的危险秘密。