Tells the same story as Full Metal Panic Second Raid and is as such, also based on the novels The End Of Day By Day. 
Leaving off after the original series, this series tells of Sousuke and Mithril as they fight Amalgam. Like the original series, but both sides have gotten a bit more aggressive...

This series is set about two months after the events ocurred in the Tuatha de Danaan at the end of the original series. Mithril becomes aware 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 intelligency 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... Like many of its fans know, it is based of the FMP novel "The End of Day by Day."
 
(Source: Anime News Network)

On her day off, Tessa wakes up in her commander chair. After regaining her composure, she notices that her favorite stuffed animal is missing and thus tries to remember what actually transpired the night before. To do so, she will spend time with all the main characters of the Danaan crew, and eventually recalls the events of the previous night. 
[Written by MAL Rewrite]

Jindai High School was a relatively safe place, right up until Sousuke Sagaka transferred there. A total nut, he wreaks havoc on the school's student body and gets into a world of trouble with the teachers! But there's more to Sousuke than meets the eye&mdash;not just a hell-raising student, he's actually a member of an elite military unit, on an undercover mission to protect the beautiful schoolgirl Kaname Chidori from the KGB. 
(Source: Tokyopop)

A sergeant by the name of Sousuke Sagara is assigned an important task. That of guarding high school girl Chidori Kaname. Sousuke is a military genius, gaining high rank at an early age, but because of his strange upbringing, he lacks social skill. Now, he finds himself as a fish out of water as he attempts to protect a girl from an evil organization and turn in his school work on time.
 
(Source: Anime News Network)

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