Mihama Academy—on the surface, a closed learning environment established to nurture students who find themselves at odds with the world around them; in actuality, an orchard-cum-prison built to preserve fruit that has fallen too far from its tree.
Yet with the arrival of the institute's first male student, the nearly preposterously opaque Kazami Yuuji, the students at Mihama begin to fall out of step with their predetermined rhythms. Will Yuuji prove to be the element the girls around him needed to take hold of their lives once more, or will the weight of their pasts prove too steep a wall to overcome?
The girls at the dormitory find themselves with a lot of guilt about learning Yūji's past, but continue to read regardless. The flashback starts with Yūji in the hospital and being visited by Asako Kusakabe and her friend JB where Asako declares that she will be his god from that point on and takes him with her to her home. Here they find all the scars from his previous wounds. At dinner Yūji accidentally kills a fly and shows signs of trauma from killing people. Shortly after, Asako is seen trying to feed Yūji but he declared that her cooking is too horrible to be considered edible. Asako gifts Yūji a dog which Yūji names John and they become constant companions. Asako trains Yūji in all sorts of things in which he takes a liking to sharpshooting. At a later date while Asako is away, the house is attacked by a bear which kills Yūji's dog. Yūji chases after the bear to save his dog but is not able to pull the trigger, specially after seeing it was just feeding its cubs. When Asako arrives he tells her that he was completely useless but Asako consoles him by saying that he is fine just the way he is. Later that day when they bury John Asako tells Yūji that he is not allowed to die unless he saves 5 people and tells him that he should become someone who can pull the trigger for others rather than himself.
Asako tells JB that Yūji is no longer a virgin and that they have been doing it many times since his birthday. Asako convinces JB to also sleep with Yūji and prevents her from backing down. Sometime later, when Asako's health begins to deteriorate for an unknown reason, Yūji ends up taking her place at some missions, which greatly upsets JB when she finds out. Eventually Yūji decides to also work for the same organization as Asako, and JB eventually agrees. Yūji and Asako travel to America and Yūji is enrolled at a military academy, where he befriends the slightly older Daniel Born. Yūji ends up constantly helping Danny with his training. When Yūji wins the first place in marksmanship, he is challenged by second place winner Milliela Stanfield to a shooting contest. When Yūji makes a shot thats impossible to Millie, she falls in love with Kazami and starts following him everywhere. Yūji, Danny and Millie are eventually assigned to the same platoon.
The episode starts with Danny's funeral with Yuuji, Millie, and Danny's family present. According to Yuuji, he had died in an accident. Flashback to their days in the army, Yuuji and his group meet with their platoon's new member, Robert Wallson aka "Immortal Robbie". Yuuji learns that the "Immortal" is mistakenly taken from the Japanese word "Imouto" which means "little sister" as Robbie is known for being an otaku who plays erotic games featuring little sisters. Later, their platoon is dispatched in a jungle where Yuuji gives a brief summary of his companions' past. Daniel Born, aka Danny, is a former car thief who was born in Arizona, Milliela Stanfield, aka Millie, was an impoverished prostitute who sold herself in bar bathrooms in order to pay for her daily meals, Robbert Wallson, aka Robbie, is an otaku who only loves two dimensional women and Yuuji who describes himself as a sniper who is unable to kill. They are later introduced to another new platoon member Edward Walker who Yuuji coached in shooting practice before and their platoon leader Justin Mikemeyer, a military physician who wishes to be called "J". After a somewhat awkward speech, Justine renames their platoon into the Bush Dog Platoon. Some time later, during one of their night missions, their platoon engages with an enemy group during which Yuuji forces himself to snipe and kill 9 people after some words of encouragement from his friends but he becomes sick and vomits with each person he kills. Despite this, his efforts saved their platoon and they all retreated safely. Eventually, he overcomes this weakness and becomes accustomed to killing in battle. A period of time passes and Yuuji returns to Japan after his platoon's duties have ended. Millie and Danny see him leave and it is revealed that Millie confessed her love to Yuuji only to be rejected yet she continues to hope and pray for his good fortune. Yuuji reunites with Asako in their old mountain home and decides to give his life to her but she quietly replies that she does not need it.
Asako's health is quickly deteriorating. Meanwhile, Yuuji is assigned to various missions by JB after he officially inherits Asako's old codename is CIRS, 9029. While on a guard duty mission in Colombia, Yuuji receives a call from JB informing him that Asako has collapsed causing him to rush home. Yuuji reveals that Asako suffers from a kind of venous thrombosis and that the original cause was a capillary rupture that happened after Asako took a shot from a high-caliber riffle. While such a condition would normally be survivable, Asako, despite her periodic treatment, regularly used booster drugs which made her body fragile. The doctors concluded that there was nothing they could do for her. Now on her death bed, Asako welcomes Yuuji home and he tries to will her into living and eventually breaks down in tears. Asako tells Yuuji to live for his own sake as he is now capable of accomplishing anything. Asako and Yuuji briefly reminisce about a brief moment in his past which he has forgotten. Asako then falls asleep and passes away peacefully. Grieving over the death of her best friend, JB recalls when they first met in an orphanage as children. She then invites Yuuji to live with her in her luxurious apartment which he does. Eventually, Yuuji decides to go on a soul searching trip which he and Asako originally planned on years ago albeit in a different location. After returning home, he visits the grave he made for Asako near their old home where decides to "do his youth over" and enroll in a "normal school" which resulted in his transfer to Mihama Academy and his current situation. As Yuuji finishes his life story narration, JB's assistant, Chiara Farrell, enters the room which prompts Yuuji to leave and return to the academy but as he leaves, his given a mission to assassinate someone called Ethan Glow but is then revealed to be Heath Oslo, the terrorist who took Yuuji in as a child after his mother died. This sudden realization causes Yuuji to lose his composure and fail his mission. He is then forcefully taken away by an unknown group. Back at Mihama Academy, the girls are shocked to see Yuuji on the news and his alleged participation in a terrorist attack conducted by Oslo.
The girls question Chizuru about what happened to Yuuji but all she tells them is a message left by Yuuji himself telling them not to look for him or to get too deeply involved if he suddenly disappears as this is how his "company" works. Chizuru gives a brief explanation of Yuuji's relationship with Heath Oslo causing Yumiko to hypothesize that the government may be using Yuuji to bargain with Oslo as he considers Yuuji to be very important. Chizuru warns them not to do anything that might worsen Yuuji's situation. She also announces that Mihama Academy will be closing soon due to Yumiko's father, the school's main sponsor, losing his position and because Makina's family has stopped giving contributions to the school. Later that night, the girls enter Yuuji's room and find diary-like entries about the girls written all over his walls and floor including one that appears to be a suicide note. JB suddenly calls them and confirms that the news of Yuuji being a terrorist is false but he is still under suspicion and is being kept in a holding facility. The girls then gather information about Yuuji and Heath Oslo using Yumiko's information network and learn that Oslo had smuggled a weapon of mass destruction into Japan. Yumiko herself confirms this when she meets one of her connections who is none other than Robbert Wallson, Yuuji's old friend and comrade in the army. Robbie, now known as James Okada, is a former intelligence operative and has opened his own soba restaurant after retiring. James reveals Yuuji's location and gives Yumiko a detailed explanation about the Thanatos System, a semi-organic computer capable of hacking into every internet-capable device and can be considered the "brain" of the nation itself. James explains that acquiring the Thanatos System is Oslo's true goal and since the government cannot hand it over, they turned Yuuji into a bargaining chip after Oslo attacked the Consulate. Meanwhile, the other girls were reflecting on their future plans. The next day, Mihama Academy officially closes and all the girls, except Michiru, meet at the school's entrance where they resolve to help Yuuji even if it means that they can never return to their old lives. After Sachi gives a farewell speech to the school, the girls prepare to leave but Michiru barely arrives after finally sorting out her feelings and all 5 of them leave Mihama Academy together. Back in the holding facility, Yuuji is introduced to the Thanatos System itself which uses a hologram to project the image and voice of his supposedly deceased sister, Kazuki Kazami.
After riding on a train, the girls arrive at their new home, a boathouse owned by Yumiko who believes it best to be able to move around, hideout and all, should the need arise. In the holding facility, Yuuji confirms that the hologram is indeed Kazuki after she answers his question. She then reveals that Oslo had smuggled a new kind of nuclear bomb that can cover a radius of 50 kilometers should it explode. She also explains why Yuuji is valuable to Oslo; Yuji is the only survivor of a human experiment to create the ultimate soldiers through various experiments, drug administration, and testing. However, the side effects of the booster drugs used on the test subjects produced adverse side effects which resulted in the experiments' deaths within 2 years but Yuuji survived thus making him a valuable project sample. Meanwhile, Michiru finds a cellphone in her bag which then rings and Kazuki's voice is heard despite the number belonging to Yuuji's phone. She introduces herself as Thanatos offers the girls her assistance to rescue Yuuji in order to disrupt Oslo's plans. Despite their doubts, they decide to cooperate with her not knowing who she really is but Amane seems to find the voice familiar but could not remember properly. The next day, Kazuki provides each of them all with special cellphones in order to contact each other without being traced. Before explaining her plan, she convinces Yumiko to admit her feelings for Yuuji in order to test her resolve. Back at the Thanatos System's holding facility, Kazuki reveals the truth of what happened to her during the bus accident years ago after Amane had escaped while she was left behind.
JB explains to her assistant, Chiara Farrell, that she has been confined due to her being the person in charge of Yuuji. She believes it is to keep her from giving an unwanted testimony and that Yuuji may be executed for his supposed attack on the consulate. She also announces that she will have a different job after her return to Langley but Chiara reasons that it is only to keep JB quiet. JB then warns her from speaking too much as they are under surveillance. Back on the girls' houseboat base, Kazuki/Thanatos announces that Yuuji will be transferred from the holding facility on August 6 at 6:00 p.m and that the girls must prepare an extremely large sum of 100 million before then. To this end, she created a series of plans in order for them to earn the amount within a day and assigns the girls to do various jobs. Yumiko uses her laptop to sell one of Makina's possessions online and uses an auction site to buy and sell. Amane rents a car and is made to memorize a very specific but complex route around the town. She once again finds Thanatos' voice familiar but cannot recognize it as Kazuki's most likely due to the fact that several years had passed since the two separated. Sacchi opens a private bank account for the girls and later accompanies Makina to a gun maker were she picks up a specially made, pink colored sniper riffle which was ordered ahead of time by Thanatos. The shop's owner, Morishima, strongly hints that he knew Asako, Yuuji's late mentor and guardian, since she was a child as Makina strongly reminded him of her. Michiru, surprisingly, was assigned the most tiring task wherein she literally traveled to different countries within the day engaging in a variety of transactions that allowed her to earn billions by following Thanatos' detailed instructions but was ultimately left with just enough money to meet the required sum after which Thanatos explains their plan to rescue Yuuji through a raid. Meanwhile, Chizuru, the now-closed Mihama Academy's principal, is seen eating in a restaurant when she too receives a call from Thanatos offering her a site for the new Mihama Academy school building which she quickly accepts. JB is seen relaxing while watching television in her quarters when her television suddenly displays a message from Thanatos saying that "the Mihama Women's Volunteer Corps YK Rescue Campaign is underway" to her confusion. Back in the Ichigaya holding facility, Yuuji is seen tied up while lying on a bed and being monitored via surveillance by guards. Heath Oslo is then seen discussing the installation of the two warheads in a metropolitan area with one of his men who explains that one has been planted while a suitable location is still being searched for the other. They then discusses their own plan on retrieving Yuuji. The next day, the day of the operation, Yumiko gives a pep talk to the girls reminding them that they were heading to a war zone where there was no guarantee of their lives and the girls eat what may be their last meal.
On the day of their operation, the girls make their final preparations; Makina rents a hotel suite where she prepares her sniping position, Michiru meets up with a member of Yuuji's organization and picks up a "toy" that Thanatos requested, Sacchi goes to the grocery store and buys ingredients to make non-explosive smoke bombs and Yumiko discusses their plans with Thanatos. Meanwhile, in a military base in Okinawa, Milliela Stanfield, now a pilot, seduces her fellow pilot in a toilet and steals his uniform. By sunset, the operation begins as Yuuji is being transferred to Akasaka to await trial. The armored car carrying Yuuji is attacked by Oslo's men who kidnap him after killing the soldiers and strap a bomb on his wrist that is set to detonate in six hours or if his vitals weaken. Makina then causes a distraction on the road takes out their cars' engines with anti-tank bullets. As they unload Yuuji, Sacchi uses her hand-made smoke bombs to blind them allowing her knock them out with ease as she is wearing a gas mask to cover her nose and eyes. As backup arrives for Oslo's men, Amane arrives as well and drives them all, along with Makina and Michiru, through the route she was taught and eventually out of the city. Along a mountainous road surrounded by a forest, they are ambushed by Oslo's men in a helicopter. Just as they are almost shot and killed, Millie arrives on a helicopter she stole from her fellow pilot earlier and takes down Olso's helicopter. James Okada communicates with the girls and explains that Thanatos' core, Kazuki, can be saved. While all this was taking place, JB arrives in the Thanatos System's room and frees Kazuki from the system with James' help and they make plans to meet up with the girls on Kazuki's "ship" that just arrived. Amane turns on a turbo feature on her car and launches them all to the sea where they land exactly on top of their houseboat, the roof of which had been greatly reinforced in order to accommodate the weight of a falling car. Just then, a submarine emerges from the sea and Kazuki appears on the deck and introduces herself as Thanatos.
Amane is extremely thrilled to see Kazuki again and becomes emotional as the latter reminds the former of the promise they made years ago. Yuuji regains consciousness inside a room and reunites with his old platoon leader Justin Mikemeyer who has been promoted to Captain. Jimmy's wife, Zoey Graham, a member of the U.S. Central Intelligence Agency, enters the room and reveals that her father, a journalist who once pursued Oslo, was one of Yuuji's dead victims when he still worked for Oslo. Zoey then admits her desire to kill Yuuji in revenge but he warns her that should he die right now, the bomb Oslo's men attached to him will explode and kill everyone on the ship. However, he declares that he will return and die by her hand after he settles the score with Oslo. Zoey is skeptical but she accepts as she does not want Yuuji to die before Oslo is killed. On the deck, Kazuki introduces Chizuru Tachibana as the ship's new owner and has it renamed as Mihama Academy. Yuuji, having recovered, meets Kazuki on the deck and asks her about her plans. She reveals that there is privately-owned island in Micronesia that once belonged to Asako who had its ownership transferred to Yuuji in the event of her death thus making him its current official owner. Yuuji then slaps Kazuki for worrying him so much for years and she apologizes. Now under considerable stress and pressure, Yuuji cries on her chest and Kazuki gives him two options: cut off his arm to remove the bomb and take refuge with her on the island for the rest of their lives or settle things with Oslo himself. She then comforts Yuuji which convinces him to go after Oslo and asks Kazuki to locate him. They then share a moment with each other. Yuuji then reunites with Millie and comically punches her in the face on reflex having learned that she threw away her promising military career for him. He then reveals his plans to face Oslo to the girls and promises to survive and return. Michiru's second personality emerges and kisses Yuuji for good luck which angers the other girls, including Millie, who then proceed to punish her as Kazuki returns and reveals Oslo's location. As Yuuji makes preparations to leave, JB warns him against fighting Oslo and explains that it was Oslo who gave Asako the bullet wound that ultimately killed her but this only fuels Yuuji's desire to fight. He then leaves with Millie on a helicopter. While en route to Oslo's base, they talk for a while about Yuuji's resolve. Back on the ship, Kazuki declares that Oslo will be able to hijack the Thanatos System in a few hours so she decides to get rid of the System which is currently running on auxiliary power in the Pacific Ocean. She then gives Michiru the task of cutting the cable that connects the System to its power source under the ocean while the other girls will search for bombs that might be littered in the area. Yumiko is tasked with searching for possible locations of Oslo's planted bombs and comes up with two places, both of which are directly connected to Oslo. In Akasaka, the top brass of CIRS called in Agnes Garrett, Yuuji's former superior in the naval academy, to give information on him. Kazuki contacts them and uses her former position as the Thanatos System's core to order Agnes to send a team to the potential bomb locations. Unfortunately, the CIRS top brass are arguing over who to send to the areas until JB enters Yumiko's room and offers to take charge on-site. Finally, Yuuji arrives at Oslo's base, kills the guard on duty, and sneaks in while silently declaring his return.
Yuuji invades Oslo's ship alone and takes out several of the latter's men. Meanwhile, Agnes and JB inform Yumiko that they are currently working on disarming the bomb Oslo planted earlier. Kazuki and Amane are seen in a dark room where the former is inside a capsule-like chamber where she deactivates the Thanatos System and asks Amane about her desire to associate with Yuuji after learning everything about him. On the deck of Oslo's ship, Yuuji meets a man who looks just like him but with white hair. The look-alike, who calls himself Du Pont, also refers to himself and Yuuji and Kazuki's brother. The two engage in an intense and fast paced fight to the death. Yuuji appears to have the advantage at first until Du Pont injects himself with a booster drug and tries to make Yuuji do the same but he refuses. With the drug boosting his physical abilities, Du Pont gains the advantage which forces Yuuji to take the drug as well. The two fight evenly but Yuuji ultimately wins and kills Du Pont. Despite his exhaustion and injuries, he finally arrives in Oslo's office. Oslo welcomes him warmly but after seeing that Yuuji has no interest in listening to what he has to say, Oslo prepares to fight and draws a katana that once belonged to Asako. They engage in combat but Yuuji, in his current state, can only dodge. Eventually, Oslo disarms and stabs Yuuji who uses remaining strength to push Oslo to his desk where Yuuji grabs a pen and stabs Oslo behind the neck, killing him. Yuuji removes the bomb that was strapped to his wrist using the key Oslo had and slowly walks away from the ship as it explodes. Just as he gives up all hope of escaping, he sees a vision of Asako and finds an exit just as the bomb detonates and destroys the ship. Two years after Yuuji's battle with Oslo, the girls have settled down on Yuuji's island. Makina is seen collecting some eggs from the chickens while Sacchi goes fishing on the beach as Amane arrives by plane, having gone to a supermarket in the mainland. Michiru is seen doing homework while Kazuki looks over her as everyone arrives, including JB and Chizuru. They reveal that the new Mihama Academy building has been finished and the girls can return to school. Meanwhile, Yuuji, who survived and took half a year to recover from his injuries, is seen fishing while talking with Yumiko who reveals that CIRS has been disbanded but a new organization will be created in its place but Yuuji has no desire to return. He then questions his survival as he believes that he is not yet meant to die causing Yumiko to tell him to live for everyone's sake, especially hers and everyone later takes a group picture togther. As Yumiko narrates and reflects on their experiences, the other characters of the series are shown to have returned to their normal lives and jobs. During the final scene, Kazuki is seen on the beach as Chizuru offers her a drink. Kazuki then takes off her metal arm and takes the drink, much to Chizuru's shock as she had believed the arm was a prosthetic when, in fact, it was actually a toy Kazuki wore because she thought it would be a funny joke causing Chizuru to remark that her jokes aren't funny at all.