This series takes place three months after the events occurred in the Tuatha de Danaan at the end of the Full Metal Panic! series. Mithril learns of a secret organization that has technology able to counter the ECS (Electronic Cloaking System) mode. This organization, known as Amalgam, also has "Black Technology", obtained from "Whispered" like Kaname Chidori, and like the other intelligence agencies, they intend to obtain more. However, when Sousuke's mission to protect Chidori is terminated by Mithril, all seems to be in place for Amalgam's plans.

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