Merida Island Base

The main protagonist of the story is Sousuke Sagara, a member of a covert anti-terrorist paramilitary organization known as Mithril. The story opens up with him saving a girl later identified as the Whispered Kudan Mira, and the main storyline begins when he is then assigned to guard Kaname Chidori. The two were instantly at odds with each other due to Sousuke’s unfamiliarity of interacting within a peaceful society, and he often overreacted in thinking everything was a threat, however innocuous. 

During the flight for a class trip to Okinawa, a group led by the terrorist Gauron, with support from the KGB, hijacked the airplane, rerouting the flight to North Korea (anime changed to: Khanka Autonomous Region), and capturing Kaname. Sousuke slipped away and got out of the plane, making contact with his superiors before rescuing Kaname. After stealing an Arm Slave and running, they were brought down by an enemy and then rescued by the arrival of Kurz who ordered them back to the airfield for transport. They missed their flight and took back to the woods, coming across an injured Kurz and bringing him along until they ran into an open field. Finding a way to contact Mithril, they were sent another AS with RV coordinates and time recorded in a message. The AS was far advanced and one-of-a-kind, known as the Arbalest. Using it to defeat Gauron with Kaname's guidance, they were able to escape. While running, Kaname fell unconscious, and awoke a few days later in a hospital in Tokyo. Melissa Mao, disguised as a nurse, gave her the cover story and left just as classmates came in to visit. Sousuke was among them, informing Kaname he would be sticking around as 'insurance.'

Two months later, trouble finds the pair once again. Sousuke's superior officer, Teletha Testarossa, shows up in his apartment, weary after a chase and with a prisoner in tow. Takuma Kugayama is a member of a Japanese terrorist group called A-21, a boy who suffers psychotic episodes and delusions, all made worse by being given a drug to make him more capable of controlling the Lambda Driver run Behemoth. Inadvertently involving Kaname in the situation, they take refuge in a nearby high school after disabling a tracker found in Takuma's arm. When they are found, Kaname and Tessa are taken captive and Sousuke is left with reinforcements that arrived just a few minutes too late. Tracking down the girls, they are too late to stop the activation of the Behemoth, and are left to run once more. The Arbalest sent to them, Sousuke is able to defeat the monstrous AS with the help of Kaname's Whispered abilities directing him to success once more. It is at the conclusion of this incident that Tessa announces herself as a rival of Kaname's for Sousuke's affections.

Another two months pass after this incident, and summer break is nearly over. Sousuke invites Kaname to a 'southern island,' which turns out to be Merida Island, the base of operations for his battlegroup. To add to her annoyance, they are redirected to meet up with the Tuatha de Danaan submarine. The sub holds its first birthday party the day before a mission where Mao ends up wounded after Sousuke failed to activate the Lambda Driver. Capturing Gauron, they bring him aboard the submarine, where a pair of traitors set him free and help him take over the bridge. While he plays a game with an American vessel, Kaname escapes him with Tessa's help and works her way to a place that Tessa directed her, where a Whispered can override anything by connecting directly with the sub. Being chased, Sousuke rescues her and apologizes for his anger after Mao's injury and taking it out on her, and leads her to where she needed. Afterwards, he heads to the hangar for what he hopes is the final showdown with Gauron, coming out victorious when the man self-detonates his AS in hopes of taking Sousuke with him, flinging him out to sea with Kaname's help.

It comes to be October, two months after those events, things still seem to be same as ever. Sousuke is sent to assist Kurz and Mao with the retrieval of a traitor, arriving late for exams to Kaname's ire. Being told so much to think of his own future, he surprises Kaname and Kyouko when he agrees to get his hair cut in a salon, though unfortunately for all involved, he loses his cool and attacks the stylist. Afterwards, Kaname invites him over to finish the haircut, and he falls asleep in her care. It is just after this, when he returns home, that he finds his orders to leave Tokyo immediately and for good, to not even say goodbye to Kaname. In the days following, he falls deeper into a depression, and his hatred of the Lambda Driver only grows. During a mission on foot, he deserts Mao and wanders Hong Kong, eventually being led to find what remains of Gauron hooked up to life support in a small apartment. He is told that Kaname was murdered which drives him to kill Gauron and escape a bomb wired to go off when he flatlines. The truth of it was that she was chased and overcame her assailant before the appearance of Leonard Testarossa. With Wraith's help after she convinced Leonard to leave the spy with her, she gets to Hong Kong in time to smack sense into him, ordering him to finish up the fight and return home with her. After this, he makes the deal to work part-time at half his salary, so that he may stay in Tokyo with her and continue to pilot the Arbalest for Mithril.

Christmas approaches, and with it, Kaname's birthday. A company offers a free cruise to the second year students of Jindai High, disguised as a charitable gesture to make up for their trip to Okinawa eight months earlier. In reality, it's a very well hidden Amalgam front with the intent to kidnap Kaname, the ship even equipped to run initial experiments on her. Sousuke's team are the only ones aware of this, thanks to clues given by Gauron before his death, and they keep it secret so there's no chance of a leak. During Mithril's seajack of the cruise ship to seize control, Alastors are let loose and Tessa is kidnapped when would-be hero Captain Sailor unknowingly sets the bad guy free. When the Alastors are finally taken care of, Sousuke sets off to retrieve Tessa, who then asks if he likes her more than Kaname, to which he replies no. A few days later, Sousuke gives Kaname her true birthday gift, and fails to muster the courage to admit his love for her.

It is late January when everything changes. Elections for the new members of Student Council are held, and Hayashimizu explains to Sousuke that without him there to throw everyone off the trail, it's likely people will start realizing that all of the incidents that happen revolve around Kaname. The very next day, Amalgam launches a coordinated attack which effectively destroys Mithril completely. The night before, Leonard visited Kaname and gave her the choice to go with him then to avoid the pain, putting her and Sousuke on the run and looking to be extracted to safety. Their transport was destroyed though thankfully left behind the Arbalest, and they had to try to escape, during which they received a message including a picture of Kyouko with blocks of C4 strapped to her chest. Sousuke left Kaname to Al and disarmed the bomb, Wraith disguised as their homeroom teacher coming to help him. When Leonard attacks in the Belial, shrapnel seriously wounds Kyouko, and Sousuke loses the fight, the Arbalest destroyed. Kaname turns herself over to Leonard to spare Sousuke's life and is taken away. While all of that is happening, Merida Island is attacked and control of it lost, though they put up a good fight and managed to escape. They're the only ones left, and most of the crew stays when Tessa announces her plans to seek revenge. Those that left were either injured or had family to support and couldn't afford a life on the run without pay.

Completely on his own, Sousuke quickly uses up his resources in an attempt to find any leads on Amalgam, coming to a small and corrupt place known as Namsak just a month later. Looking for a former comrade in the AS Arena fighting circuit, he finds the man was just killed, and takes his place on the team, growing close to the team leader Nami and their new benefactor Michel Lemon. After a month passes, he is finally able to get an invite to the secretive 'Yami Battle,' which he knows to be monitored by Amalgam, while Lemon is left a prisoner. Lemon rescues the crew of Crossbow, exposing himself as a member of the French DGSE, and Nami is killed by Kurama when Sousuke hesitates on leaving his AS following his win. A manhunt ensues, and Sousuke is seriously wounded, though he manages to do the same to Kurama, learning possible locations of Kaname while they both lay dying. Sousuke's last memory of that moment is Lemon calling out for epinephrine as he slipped out of consciousness.

Tessa is found wandering the streets of San Francisco and taken in by a mental ward for her seeming delusions of having been mutinied against by the crew of the TDD. This was a ruse to draw out Amalgam, and they are able to get some information to know where to find Leonard. While this is going on, Sousuke wakes up 56 days after the final events of Namsak, a prisoner of the DGSE in a secret hideout. They're attacked and only he and Lemon escape, both wanting revenge against Amalgam. Sousuke recommends they visit an old friend in Florida, able to train back into fighting shape and gain control of an M6A3 Dark Bushnell for their raid on the villa in Mexico where Kaname is being held. Mithril and Sousuke's raids are planned at the same time, and Sousuke reunites with Kurz and Mao. Sousuke loses his AS and is thrown off when he finds that Kalinin has turned traitor and is fighting against him to keep Kaname in Leonard's custody. When fleeing the villa, Leonard gives Kaname his revolver and tells her if she really wants to escape, then to shoot him and do so. She refuses to kill him, and when he grabs her, she accidentally squeezes the trigger and shoots his head. In shock, she is unable to take the time to escape, retrieved by Kalinin and taken away in a helicopter. Behemoths are dispatched to the scene, and Wraith delivers a surprise to Sousuke, the new AS Laevatein equipped with Al, built with the help of the Whispered Kudan Mira. He quickly dispatches the enemy, and he is contacted by Kaname over an open channel, where she begs him to find her no matter what, and they promise to kiss when reunited.

It's quite a few months later, and Yamsk11 becomes a place of interest. An old, decaying underground city in Russia, it was the birthplace of the Whispered, and a source of interest for both Leonard and Tessa. Revealing himself as alive to Kaname, Leonard no longer treats her kindly, hitting her and speaking cruelly and forcing her aboard a helicopter along with captive Lemon. Tessa and Sousuke go to the place at the same time, and they all get separated from their groups. Kaname helping Lemon limp along meets up with Tessa, and the three go to find the central location that is the source of the Tau waves responsible for the Whispers. Meanwhile, Sousuke runs into Leonard, who begins to make him unsure of things when he speaks of his plan to make the world a place of peace, where all of the cruel deaths never happened. On the surface, Kurz chooses the wrong location of Casper, giving away his position and taking a serious injury.

The girls find what they were looking for, and while Tessa plants an explosive, Kaname is overtaken by the consciousness that Whispers to them, the girl named Sofia, and takes her hostage instead, leaving just as Sousuke finally catches up to them. In a last effort to save them, Kaname makes all involved believe that she killed both Tessa and Sousuke so that Sofia will leave them alone and flee. Lemon describes the event as Sousuke and Tessa just suddenly falling unconscious and Kaname leaving calmly. As the three escape, they're stopped by Casper, and Sousuke is contacted by Kurz who asks him to draw Casper out of the AS. Doing so by acting as though he'll kill Tessa if not, Kurz pulls off what he expects to be his final shot, left behind as they escape the hot situation.

Another few months pass and everything comes to a head. What remains of Amalgam after Leonard's overly aggressive power grab plans to launch a 3-pronged nuclear attack from Afghanistan. It's made known that the head of Mithril, Sir Mallory, was actually a high ranking member of Amalgam by the codename Mister Mercury, and that he created Mithril to combat Amalgam when they lost sight of its ideals and the web-like power structure allowed it to be corrupted. Sofia/Kaname has completed the Telechrono Alteration Reactor Transfer and Response Omnisphere (TARTAROS) on Merida Island, and is preparing to activate it to change the recent history of the world. Tessa disbands what remains of Mithril when she is unable to make the choice to take everyone to Merida to stop the TARTAROS instead of to Afghanistan to deal witht he nuclear threat. Most of the remaining crew either goes home or to Afghanistan, while a skeleton crew accompanies Tessa and Sousuke on the TDD to Merida Island.

In Afghanistan, they are met with opposition, and barely defeat Sabine and Fowler with Kurz's help, announcing he had been retrieved by Wraith and nursed back to health while in the Russian GRU's custody. Sabine redirects the missiles to Merida Island out of jealousy of Leonard's obsession with Kaname, and one missile launches before Mao is able to stop it.

On the approach to Merida, the TDD sustains damages and Sachs is killed when trying to make sure the final preparations of the Laevatein and the jerry-rigged XL-3 Booster were truly usable. Sousuke launches and quickly takes out the Behemoth barricade, the only opposition giving him issue being the Belial piloted by Leonard. Over an open channel, he yells at Kaname, trying to bring her back to the surface by taunting her, and she is able to break free of Sofia's control thanks to his harsh words. Against Leonard, he uses the Fairy Feather designed by Kaname to make the Belial unable to use its Lambda Driver, though the machine is still powerful even without it. Unable to defeat him in those few short minutes, Sousuke is forced to abandon Al and use cover to escape, ultimately defeating the Belial with just an RPG.

​During their fight, Kaname is shown the losing parts of the battles going on by Sofia, including what she believes to be Sousuke's death when the Laevatein is destroyed, unable to see his escape from the unit. She is also shown a happy version of her life, where her mother is alive and her family all living together in Tokyo. Sousuke is a normal boy, a computer geek, and he confesses his love to Kaname so easily, promising them a good, easy life together. In spite of all of this, Kaname is unable to agree to any of it, and she refuses to activate the TARTAROS and Sofia leaves her in the face of such defeat.

Leonard, surprised by his defeat, plans to destroy the TARTAROS and take everyone with him, but is killed by Kalinin who is escaping with Kaname, the only chance of getting his family back. Sousuke chases after them, and the helicopter they tried to escape on is thrown off course, Kaname dropping from it a few feet above the launch pad and retrieved by Tessa and the crew storming the base on foot. They escape with her, while Sousuke and Kalinin have their final fight. Unable to kill the man who was like a father to him, shrapnel from the crash does it for him, and Sousuke returns to where he left Al, climbing in what remains of the cockpit and awaiting the arrival of the nuclear blast to die alone, with only a video recorded by his classmates to watch and not even enough time to finish it.

A week or so later, Kaname returns to Tokyo and goes to attend the graduation ceremony of her class at Jindai. Tessa buries Leonard with their family and discusses future plans with Lemon and Borda. The former Uruz team plans to storm an American base in Japan where they find Sousuke is being held after miraculously surviving the nuclear blast when Al activated the Lambda Driver on his own, and then having been retrieved by the US military. He is escaping at the same time, the husk containing Al with him, and he steals their Jeep while asking them to take care of Al, saying he has somewhere to be. Making it to Tokyo for the graduation moments after Kaname, the two share their kiss at last in front of the entire class.