Humanity has successfully colonized all the planets in the Solar System, with intentions to continue into new frontiers. Individuals live stable lives in these colonies, including young high school students living in 4th Tokyo on Mars. Two of these students are Iris Shirazaki and Mizuki Sera. Iris is finishing her last year of high school while studying to be a test pilot while her friend Mizuki also works as a mechanic on the aircraft. Her own brother, Kaito, oversees Mizuki and Iris as their homeroom teacher and program director.
Everyone at the Kirishina Academy is waiting for the new transfer student. Just who in the world is he, and why is he not there yet?
The transfer student, Nagisa Kiryu, is finally introduced to the other students. They can't help but feel that he is hiding something…
There is a new person at A-TEC. She is from Budget Control in Accounting. What kind of changes will she make? Will Kaito and his students be okay with these changes?
Kaito seeks the backing of the Kirishina Corporation's union to try and avoid downsizing. Unfortunately for him, Nagisa knows precisely how to handle the situation.
The students are having fun on their well-deserved graduation trip. However, Nagisa is still determined to put an end to A-TEC.
Nagisa rejects a request for additional funding, telling Kaito that with his back against a wall, he should become more innovative. Later, Nagisa fails the class exams, criticizing the subjects taught in the class. Nagisa fails the makeup exams that afternoon as well, and decides to stay afterwards to attempt to study. Mizuki comes to offer her assistance, while Kaito goes drinking with A-TEC's former chief. Both groups begin a conversation about Nagisa's upbringing. Nagisa is not truly a member of the main Kiryu family, and his brothers treat him terribly as a result. Nagisa is also the last living member of the Shinomiya family, which formed Kirishina alongside the Kiryu family, putting Nagisa in an interesting position in company politics. With the help of the entire A-TEC class, Nagisa passes the makeup exams.
While the students are finishing up the X-3 engine, they realize they need a final, very expensive piece. Angelina (a.k.a. Hanako Hattori) and Iris attended a pilot conference, and miss their flight back to Mars. Nagisa arranges for the two of them to board a private company plane, carrying a famous space engineering professor. Hanako and Iris realize the space plane has been hijacked, which is relayed to Nagisa and Director Kiryu. Nagisa doubts that the director will handle the situation and asks A-TEC to save them. With A-TEC's help, Hanako and Iris secure the cockpit and set course for Mars. A hijacker tries to shoot at Iris, but the shots end up shattering the front window. This triggers an old memory within Iris, becoming helpless as the plane veers on a crash course. Suddenly, an unknown ship saves them, while Nagisa is perplexed as to who sent that ship.
With general elections coming up, the two largest political parties, Seimin and Oozora, use favors within Kirishina to rally support for their respective candidates. The students prepare their attraction for the upcoming school festival, a rocket being propelled by a pressurized bottle of water. While testing the rocket, Iris has flashbacks of a terrible memory, and becomes sick. Nagisa asks Iris if not knowing her past bothers her, and she responds that she has nothing to complain about. The students' festival attraction goes over fairly well. Nagisa and Hanako try to figure out why money budgeted for A-TEC keeps disappearing, and after meeting with Director Kiryu, his suspicions are confirmed, and he begins to set his plan in motion.
The day before the general election, Nagisa contacts Director Yuji Kiryu, telling him to turn on the TV and that his plan is now underway. The candidate for the Seimin party, Furabayashi, moved over to the Oozora party, to most people's confusion, with the party declaring their support for him, abandoning former candidate Murakami. Upon hearing the news, A-TEC's students feel like their souls have been crushed, as the candidate that pledged to support them is all but out of the running. Angelina reveals Nagisa's plan to A-TEC, showing that he persuaded Furabayashi to change parties at the last moment. Kaito berates Nagisa, stating that he's disappointed in Nagisa, and that Nagisa doesn't seem confident in his actions. Yuji Kiryu loses his position as director, and the CEO, Kazuhisa Kiryu, prepares for an oncoming battle with Nagisa.
Nagisa is added to the board of directors, taking Yuji's spot. The A-TEC class comments on Nagisa's recent actions, unsure how to feel, while Kaito encourages them to continue pushing for A-TEC's survival. Nagisa discusses the internal politics of the board of directors with his collaborator, company Vice President Yanai, although some of Yanai's comments about CEO Kazuhisa Kiryu made him uncomfortable. Nagisa tells Yanai that to help overthrow Kazuhisa, A-TEC should be kept running. A-TEC's X-3 rocket has a test flight on September 26, but as Iris is piloting it, her repressed memories haunt her once more, and she realizes that she is Nagisa Shinamiya. The Seimin and Oozora parties unexpectedly decide to form a coalition, nullifying Nagisa Kiryu's trump card. As Nagisa calls a vote about disbanding A-TEC, none of his allies stand with him.
While Mizuki begins to nurse Iris back to health in a hospital, Dr. Jason Li finds Kaito, and brings him to a secret research facility. CEO Kazuhisa tells Nagisa his plan to open a military weaponry division, but that he needs Nagisa, Kaito, and Dr. Li to manage it. He also reveals that Nagisa is not even a member of the Kiryu or Shinamiya families, and was instead a decoy as the real Nagisa Shinamiya escaped Mars. Iris, her memory fully returned, attempts to seek out Nagisa. The CEO tells Nagisa to forget his revenge plan and join his side, and Nagisa, lost in his thoughts, finds Mizuki and breaks down. Mizuki tells him they will struggle together, and they kiss. Nagisa and Kaito, not wanting to join the weaponry division, decide to throw a wrench in their plan and re-create A-TEC. Three days later though, Nagisa gets stabbed by former director Yuji Kiryu in a dark city street.
Nagisa wakes up and finds himself in dark room, after that he is verbally abused by Yūji. Hanako goes to see CEO Kazuhisa in person, but she then realizes that only the A-TEC team members can solve this problem by themselves. ATEC's members have a plan to save Nagisa and try to put it into an action. In the meantime, in the process of investigating Nagisa's whereabouts, Kaito comes across a plan to "re-create A-TEC", a guidebook which Nagisa had prepared for a presentation, he then makes a plan to prepare for the presentation and to recapture Nagisa. By exploiting Nagisa's connections, Hanako heads down to Coldwood to look for a helping hand. At Kirishima warehouse, as Yuji tries to launch a rocket with the X-3 engine with Nagisa at Coldwood, the members led by Hanako come to Nagisa's rescue. In the console room, Hanako, who tries to stop the rocket launch, is shot by Yuji, leading to a failure of the plan.