某天，A-TEC准备迎来新的伙伴。但此时却发生了转学生在前往火星的途中遭到诱拐的事件。判断只能凭借自己这些人来渡过难关的室长濑良海斗，和A-TEC成员们一同展开前所未闻的救援作战。但，终于现身的转学生·雾羽渚的真实身份竟然是自己的上司。渚宣告若是A-TEC再继续维持高成本的累赘部门的话，就要进行裁员，并将部门解散。

迟到的转学生·雾羽渚。冠名为创业者一族的这个男人，刚刚就任为先行技术开发部部长，就对A-TEC众人宣告裁员。在他对动摇的学生们的蔑视之下，A-TEC立刻就被临时停业。此时，电视上播放了有关A-TEC的纪录片节目。走投无路的濑良海斗，被自己也有出演的纪录节目中自己的话语所激励，为了升起反击的狼烟而前往渚的办公室。

渚的哥哥专务董事雾羽雄二宣告要削减A-TEC的预算。对于雄二的行动感到可疑的渚，将身为自己亲信的经理专家安琪莉娜叫来了。她那彻底的财务管理进一步将A-TEC逼入绝境——。但，那同时也是A-TEC财务改善的延命措施。渚真正的目的究竟是？之后，失去容身之地的A-TEC成员一个接一个地从海斗身边离开了。

没有工厂，没有钱，没有同伴——。海斗带领的A-TEC完全走到了绝路。但此时雾科公司的工会向海斗伸出了援手。海斗向工会恳求从经营人员手中守护A-TEC，工会也约定进行全面协助。但，瑞季对于渚对自己的忠告“工会并非如你们想象那般纯洁正直”这句话感到耿耿于怀。

A-TEC出发前去修学旅行，渚和安琪丽娜也一同前往。A-TEC众人尽情享受了大海以及温泉，得到暂时的休息。但此时却发生了麻烦，渚的平板电脑坏掉了。而且渚有着非得在今天之内完成不可的业务……。为了将渚从绝境中拯救出来而挺身而出的人竟然是伊莉丝。伊莉丝开着轻型卡车，带着渚前往邻镇的办事处。

雾科学园的定期测试开始了。但面对A-TEC专门领域的测试，至今为止一直专注于商务的渚陷入了始料未及的苦战。对此看不下去的瑞季，以让渚说出自己的过去为交换条件，主动担任他的教师。两人在夜晚的教室留下学习。但，在听到渚所言及的自己的过去时，瑞季不禁失语。

A-TEC的学生们进行了旨在提升性能及降低成本的学习会。替代损毁的X-2的新型试作机X-3的开发，也在低预算之下想方设法进行筹资。此时，伊莉丝为了接受测试飞行员的授课，和带队的花子两人一起出差。但，错过回程航班的两人，在偶然乘上的雾科社用机内被卷入了麻烦当中。

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.

Nagisa is on course to collide with a satellite! Iris is the only pilot who can save him, but she has to overcome her own fears first!