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?
As part of the organization Mithril, Sergeant Souske Sagara, Melissa Mao and Kurz Weber recieve a secret mission: guarding Kaname Chidori, a popular student from a school higher in Tokyo which has a hidden military potential.
Sousuke is set on his mission to protect Kaname, and attacks anything vaguely resembling a threat to Kaname. This leads to funny situations and Sousuke has to explain Kaname why he is following her, blaming coincidence.
Sousuke gets oriented in his Garbage Duty and Kurtz gets to know the targets a little better. Meanwhile Tessa takes care of a research center in Russia. Sousuke's team encounter a mysterious man climbing to Kaname's balcony.
The airplane with Sousuke, Kaname and 400 of their classmates is hijacked and brought to a secluded location. Kaname is taken away from the plane, but what will Sousuke do to rescue her?
Sousuke comes to Kaname's rescue, and the rest of the rescue team arrive on the scene, as well, but can they hold off the army and save the students? Can Sousuke get Kaname to safety?
As the rescue team has left, Sousuke, Kaname and Kurz try to figure out a way to get back to safety.
Sagara and Kaname barely escapes from the enemy. Now on the run they try to find a way out. Deep in the forest Sagara isn't able to move much more with his injuries, so Kaname decides to stop and rest for a bit. After Sagara was able to stop the bleeding, Kaname realizes how dangerous and mysterious Sagara really is. To make matters worse they find an unexpected person along the way, it's Kurtz, who looks badly beaten by Gaul. As the 3 try to make to the shoreline they find themselves in a tight pinch; the forest ended and all there is now is plain fields. Not Knowing what to do Sagara had only one idea left - to have himself and Kurtz distract the enemy force while Kaname makes a run to safety. But Kaname refuses to leave.
Putting the tumultuous experiences in Khanka behind them, it’s business as usual back at Jindai High School. On the way to school, Kaname is asked out by Shirai, even offering to leave his girlfriend, who watches the debacle furiously from cover. After Sousuke threatens to kill off his family if he goes near Kaname again, the situation appears to be resolved-or is it? At school, Kaname gets the strange feeling that she’s being watched. The situation explodes when Sousuke finds foul graffiti written about Kaname scribbled on the men’s room wall, and proceeds to torture and interrogate Shirai trying to get him to confess. Kaname is called in by Kyouko to defuse the crisis before Shinji’s bladder bursts.
Once Shirai is rescued from getting intimate with the toilet bowl by his enraged girlfriend Mizuki, Sousuke sets out to learn about love from one of Shinji’s dating simulators. Kaname and Kyouko watch with distain as negotiations break down between Sousuke and his virtual love. While Sousuke hasn’t got a clue about romancing virtual girls, this military maniac is about to find himself on the receiving end of a crash course in the real thing courtesy of Mizuki Inaba. Blaming Kaname for Shirai breaking up with her, Mizuki recruits Sousuke to fill the roll as her beloved boyfriend in the hopes of convincing some old friends from Jr. High that she has the perfect relationship. Will Sousuke survive basic training in the art of romance? And just how much of this insanity is Kaname going to stand for?
Attempting to clear Japanese customs at the airport, a peculiar young man named Takuma Kugayama lunges at and viciously attacks a customs agent for simply having a crooked tie. Elsewhere, Melissa and her team raid a terrorist base in a dense forest with their M9’s, only to learn that the target they’ve taken down isn’t the one Mithril was hoping for. Back on de Danaan, Captain Testarossa is distressed that the terrorist organization A21 has escaped her grasp. While this raid was a bust, information comes in that a member of A21 has been taken into custody at Tokyo airport, and that the prisoner may be a Whispered. Lt. Kalinin takes off to investigate.
Chidori does not quite believe that Tessa is Sagara's superior as Tessa is having fun acting blonde. Meanwhile, Kalinin is being interrogated by Takuma's 'sister' and learns the history of A21. When Sagara discovers a sensor on Takuma, the group moves to the school to wait for back-up.
In the room, Tessa manages to build a rapport with Takuma. The girls are captured by A21 while visiting the washroom and the group forces Sagara to make a choice over who to release first. Considering that Chidori is more athletic even though the second person will be in more danger, Sagara asks for the clumsy Tessa to be released first. When it's Chidori's turn, she grapples with Takuma half way through. A shoot-out occurs and both girls are captured while a mini-torpedo hits the spot which Sagara is hiding in.
A21 has recovered Takuma and taken Kaname and Tessa hostage! The girls fear Sousuke may be in a bad way, but our intrepid Sergeant has managed to survive the RPG attack with just a few scratches. With Kurz and Mao now on the scene, priority shifts to retrieving the hostages and putting a stop to A21’s plans. A21 takes Kaname and Tessa back to the freighter where Lt. Kalinin is being held in order to use them to get Kalinin to tell them what he knows of the Lambda Driver. Imprisoned, Tessa laments over the situation, but takes courage from Kaname’s strength and resolve not to let it get her down.
Kaname and Tessa are taken to Lt. Kalinin at gunpoint, where they demand information about the Lambda driver or the girls will be shot. With a bit of deception and help from Tessa, the interrogator is subdued and the hostages move to make their escape, but first, they must confirm what lies in the ship’s cargo hold. This suspicion about the Clinton’s cargo is confirmed. A colossal AS with tremendous destructive power is anchored below deck. They have little time to gawk, as Seina, Takuma, and their guards confront the gang. Just as things about to turn bad, Sousuke and Kurz bust in and take the fight to the guards. They manage to wound Takuma, but its not enough to stop him from reaching the Behemoth’s cockpit.
With the ship sinking under Behemoth’s enormous weight, Kurz and company move quickly to abandon ship. Clearing the cargo doors and crashing onto the dock, the group watches helplessly as Behemoth crushes Mao’s M9 like an empty beer can, then sweeps aside a squad of JSDF-96’s. There’s no time to worry about Melissa though, as Takuma and the Behemoth set their sights on Tessa and the rest of our heroes. Behemoth pursues the truck through the city, spraying 20mm cannon fire in the vehicle’s wake. Desperate to stop Behemoth, Tessa orders the launching of the ARX-7 Arbalest that Commander Mardukas had prepared for just such an occasion.
With the Arbalest inbound via ballistic missile, Kurz has had enough of being shot at and decides to try something daring. Breaking out his sniper rifle, Kurz draws a bead on the Behemoth’s head Vulcans and manages to disable half of them. With the Arbalest on the scene, Sousuke bails to take to his AS and combat the giant, but getting at his AS will prove more of a challenge than he’d like. With a little bit of luck, Sousuke manages to board the Arbalest and take the fight to the Behemoth. Despite the Arbalest’s battle capabilities, the Behemoth is going to be a tough nut to crack.
The Danaan is in the shop, and Captain Testarossa is feeling pretty bummed about it. To lighten the mood, Mao drops by Tessa’s office, but by the time Tessa arrives, the place is littered with empty beer cans and cigarette butts. Needless to say, Tessa isn’t pleased. The situation quickly spirals and Tessa ends up challenging Melissa to an AS duel, with the stipulation the loser has to run around the base naked. Kurz is obviously pleased by the news and clears his schedule to witness that spectacular event. Tessa, being all talk about her “fearsome AS piloting skills”, recruits Sousuke to train her how to operate an AS. Sousuke’s definitely going to have his hands full in more ways than one.
Shinji and Sousuke have dragged Kaname, Kyouko, and Mizuki to the Narashino Ground Self-Defense Force Post Festival. Alas, Kaname’s dreams of swimming, beaches, and summer romance have been dashed once again. Sousuke meets Shinji’s father, who is the ranking Secretary at the base. Shinji seems embarrassed, but Sousuke’s his usual military-minded self. Elsewhere, the girls are getting hit on by one of the soldiers from Nerima who came to compete in the AS competition against Narashino. Apparently Narashino’s AS unit is a joke, lacking any decent combat skills, and Nerima has defeated them soundly every year. Kaname turns the pilot’s offer to go AS down, and Mizuki rages over the fact he didn’t even notice her.
Kaname’s finally getting her summer fun, but she doesn’t seem too thrilled about it. A few days prior, Mithril Intelligence obtained information that an arch nemesis Sousuke knows very well is alive and wandering the barren wastelands of Helmajistan. While Captain Testarossa is against the idea, Intelligence deploys Sousuke, along with a Mithril unit based in the Indian Ocean, to Helmajistan to assassinate this dangerous target. On the flight over, Sousuke gets heckled by some of his “comrades”, making it a very unpleasant flight for our young Sergeant. Eventually, the team arrives in theater and parachutes in country.
The Mithril assault team finally begins to take Sousuke's advice into account, but it may be too late: Gauron has one of Sousuke's old comrades predicting what Sousuke will do.
Zaied outwits Sousuke's team and interdicts their advance! Zaied's team surrounds Sousuke's team who is carrying a nuclear warhead. Zaied moves first. While Sousuke is fighting against Zaied, Gray and the team are aghast at the power of Gauron.
Sousuke spends most of the budget for the school festival. Kaname gets so disappointed. It might have been his apology? He invites her to "go to a southern island", but the destination is not what she is thinking...
Flashbacks of Kurz and Sousuke's time as trainees.
The De Danaan is heading toward Melida Island when it receives an emergency contact. Gauron's troops have appeared at Beridaobu Island! This island is the US military's chemical weapons base. They have Gauron's new AS, Venom, rampaging around and also the latest mass production model, known as Shadow. Things start to get tense for Sousuke and the others.
Gauron manages to escape thanks to the betrayal of two soldiers. Gauron takes Kaname hostage and takes over Dana, the AI of the De Danaan.
Trouble brews on the Tuatha de Danaan. Gauron has taken control of Dana and isolated the crew into the back half of the ship. Tessa and Kaname are held prisoner on the bridge, helpless to stop Gauron.
Kurz and Sousuke, free to roam the mostly empty ship, fight to free the contained crew. Meanwhile, Gauron is getting desperate.