Kaname Chidori is your average teen in modern Japan. At least, that's what she thought before a boy named Sousuke Sagara began following her around, acting like a totally paranoid military freak!
Things start to be explained when her school trip is hijacked and taken to North Korea, where Kaname is kidnapped and told that she is a Whispered. the Whispered are genetic anomalies, beings born with vast amounts of incredibly advanced knowlegde of math, science, and technology. Sousuke comes to rescue her, revealing that he is a trained specialist in the secret military organization MITHRIL, sworn to protect the world and guard the Whispered from being misused by terrorists.
Now with the knowledge of what she is and what Sousuke was sent to do, can she make her way through high school in one piece?
Mithril and the SRT rescue refugees from a city torn apart by civil war. However, during the fighting, they discover that the enemy possesses advanced weaponry rivaling their own. They surmise that a highly funded, well-equipped organization may be supplying their enemies.
Sousuke and Kazama investigate who is posting embarrassing and revealing picture of Kaname on the Internet. Meanwhile, Amalgam operatives, led by Gates, extract their payment from their military clients.
In Nanjing, Amalgam kidnaps peace delegations from Northern and Southern China and fortify themselves in an underground tunnel beneath the Yangtze River. Mithril attempts a rescue in the tunnel's dangerous confines, but falls into Amalgam's trap.
Mithril is perplexed at how the enemy is able to follow their movements. Once they realize that their communications have been compromised, Tessa and Kalinin give false orders to facilitate the rescue and turn the tables on Amalgam.
The SRT travels to Sicily to capture the traitor from the Nanjing operation. Sousuke has difficulties balancing work and school when he tries to have a phone conversation with Kaname and drive the getaway vehicle at the same time.
Mithril attempts to learn more about the mysterious Amalgam organization. Kaname and Sousuke's relationship begins to blossom; however, Sousuke is reassigned to another mission and is forbidden to see Kaname.
Sousuke argues with his replacement about the mission to protect Kaname. Kaname wonders why Sousuke does not come to school, and starts to become worried. When she needs to see him, she finds out that his apartment is vacant and he has disappeared.
Tessa berates Sousuke for emotionally involving himself with Kaname and neglecting his other duties. The SRT receives a new leader who stages an AS duel to help Sousuke properly operate the Arbelast.
Kaname confronts the Mithril operative sent to replace Sousuke; however, as she is about to get answers, she is attacked by an Amalgam assassin. Kaname outwits her pursuer until Leonard Testarossa, another Amalgam agent, shows up and kills her assassin. He reveals that the assassin was a rogue agent acting outside of Amalgam's interests.
Sousuke and Melissa are deployed to a divided Hong Kong in a team made up of SRT/PRT personnel of East Asian origin to locate an Amalgam Codarl (m)-type Arm Slave attacking North and South Chinese army units, but Sousuke's feelings for Kaname places his MITHRIL comrades nearly in danger, earning a sermon from Melissa.
While Sousuke continues to wander in Hong Kong, Tessa is "forced" by Admiral Borda to deploy her M9s to the island after sightings of the Codarl (m)-type Arm Slave were confirmed.
Sousuke meets Gauron, now crippled and about to die while Xia Yu Fan combats an SRT unit lead by Closeau in downtown Hong Kong as tensions continue to mount between North and South China.
Kaname makes a surprise visit to Sousuke in Hong Kong, and assists him in using the Arbalest's Lambda Driver to the fullest. Sousuke defeats Gates once and for all, then returns to Tokyo--and high school--with Kaname.