In Kaminoyama High School, animation club members and good friends Aoi Miyamori, Ema Yasuhara, Shizuka Sakaki, Misa Tōdō, and Midori Imai promise to each other that they will make an animated feature together one day. Two and a half years later, Aoi is working as a production assistant at Musashino Animation, an animation studio that is currently working on an upcoming anime for the fall season, called Exodus!. She visits Misato Segawa, the animation supervisor for the anime's fourth episode, to retrieve the checked animation. Then, she drives to the studio, where she attends a meeting as the entire crew (including Ema, who is a key animator) watches the premiere of Exodus!. When the anime premieres, it is met with a lukewarm public response, to everyone's relief. Later on, while previewing the third episode, the crew finds that Tarō Takanashi, another production assistant, was unable to finish the key frames in time, thus leaving the quality of the episode's animation erratic. Since there are no other key animators available to finish the frames, the crew turns to Segawa, who reluctantly decides to take the extra job at the request of the third episode's animation supervisor Ryōsuke Endō, who is her rival. Once the frames are finished, Aoi retrieves them before taking the animation director, Hironori Madoka, to a dubbing session. She then stops by Segawa's house and finds her lying on the floor unconscious.
After tending to Segawa, who had collapsed due to severe dizziness from a fever, Aoi manages to get Ryōsuke to handle the key frames for episode four. As the production process continues, Ema calls Shizuka, who is now a restaurant employee and also a beginning voice actress, and the two make plans for the group's monthly get-together event. Ema then notes to Shizuka that she and Aoi are interacting less at work, and Aoi seems to have an overwhelming workload, being responsible for the production of two episodes. Later on, during the sound design process of a later episode of Exodus!, the director, Seiichi Kinoshita, becomes dissatisfied with the design of one of the characters. He then suggests making changes to the character's design based on his vision of her, which involves completely new ideas that were not incorporated during production.
General animation supervisory assistant Yumi Iguchi is impressed by the new iteration of the 4th episode & decides to begin work on the retakes. Aoi is faced with a heavy workload regarding the 4th & 9th episodes. After Rinko checks the key frames, Aoi sends them to in-between inspector Chiemi Dōmoto, then realizes she mistakenly sent one of the cuts to the camera department. She finds that one of the key frames she requested has not been delivered to her & calls lazy freelance key animator Mitsuhide Kisa to finish the cuts. Although he begins work, the process is delayed due to his laziness. The missing key frame is stuck on a truck being held back in roadworks. On the day before episode 4 is due to air, a problem with the studio's FTP server results in the delivery of an external studio's color shots getting delayed.
As Shizuka goes in for her first audition at Prussia Studio, she becomes nervous about going up against popular voice actress Rina Sōma. When she is the next one to audition, her nervousness gets the better of her, although the director is impressed. Meanwhile, Aoi receives a call from her mother, who congratulates her on her work on Exodus! despite her confusion about the story, and informs her that her father was also impressed. The scene then flashes back to the time Aoi, Ema, Shizuka, Misa, and Midori presented their club's anime back in high school; although the students were unimpressed by it, the five of them still found pride in their work. The next day, Aoi, Ema, and Shizuka meet up with Misa, now a 3D computer graphics operator, and Midori, a college student who is aspiring to be a scriptwriter. Together, they watch a movie, visit the park, go shopping, and get some drinks. While at Shizuka's workplace, Aoi, Ema, and Misa tell each other about the hardships they are experiencing at work, while Shizuka laments that she has not done anything significant in her work and that she did not do too well on her audition. Later on, Aoi receives a call from Tarō, who asks for her help, but when he goes off-topic, she hangs up on him. When the get-together ends and Aoi and Ema ride the train home, the former remarks that she does not have a concrete anime-related goal in mind. While walking home, Aoi receives a call from Tarō, who again tries asking for help, but she hangs up on him. The next day, things become hectic at the office with Seiichi being behind on storyboards and Ryōsuke deciding to drop out of directing the eighth episode following an argument with Tarō.
Tarō tries to reason with Ryōsuke and his decision, but he refuses to listen. Tarō then vents his anger to Aoi and blames her for the situation, explaining that the argument was the reason behind the phone calls. With the storyboards for the final episode way behind schedule, being a month late, chief production assistant Yutaka Honda, desperate for progress, goes to extreme lengths and locks Seiichi inside a cage in the storage room in order to get him to finish them, despite his protests. Tarō explains to Aoi that he got caught up as the middle man between Ryōsuke, who wanted to do the key frames for an explosion scene, and the 3D director Yūichirō Shimoyanagi, who had already prepared a CGI explosion, the result of which led Ryōsuke to believe people were favoring 3D over 2D and drop out of directing the eighth episode. An unsatisfied Aoi accuses Tarō of not handling the situation better and tries to tell Honda about it, but he talks her out of it. Caving under the pressure of his new work environment, Seiichi recounts how his once successful career as an anime director took a downfall after the release of Jiggly Jiggly Heaven, and it is revealed Exodus! is his first official anime in six years. Whilst having a drink with his coworker Hotta Hikari, Ryōsuke learns from animator Saburou Kitano about how he is teaching 3D animators himself, stating that it is not about whether 3D is better or not, but rather how it can be used to improve the quality of anime. Aoi and Ema meet up and eat at the latter's house, where they talk about how 3D is continuing to influence the production of anime, which is what led Misa to choosing her career path. The next day, while showing Ryōsuke the 3D-rendered scene of the explosion, Aoi learns that the beginning of episode nine, which follows on from the explosion in the eighth episode, had been finished using key animation.
Despite seeing the 3D-rendered explosion scene, Ryōsuke refuses to return to work, citing that things had already gone far enough. Becoming agitated by Tarō's attitude, Aoi finally informs Honda of his failure to handle the situation between Ryōsuke and Yūichirō. Honda decides to tell Seiichi about the situation as well, but discovers that he had somehow managed to escape his confinement so he could sneak off to the after-recording session. Meanwhile, production assistant Tatsuya Ochiai is given an offer by his friend, line producer Houjou Hiroaki, to work at Studio Canaan, another anime studio, but Tatsuya turns down the offer. Later, Aoi and Erika discuss the possibility of hand-drawn animation being phased out by 3D animation completely. Aoi then hears from Misa about how, even as a 3D creator, she needed to study up a lot of hand-drawn animation to get an artistic sense.
While preparing to leave for Musashino Animation, Aoi learns from her sister, Kaori, that she is coming over to stay, and she subsequently entrusts her house key to Midori. During the Musashino Animation morning assembly, Tatsuya announces that he is leaving at the end of the week, citing personal reasons, which shocks Aoi and Tarō. After the assembly, Honda reassigns Erika to continue Tatsuya's work on the eleventh episode, which leaves Tarō to continue her work on the twelfth episode. As a result, Aoi is put in charge of work on the final episode, which Tatsuya recommends as a good advancement for her experience. Aoi later learns from Masashi Yamada, the animation director for the fourth episode, that Tatsuya had eventually accepted the offer to join Studio Canaan and work on their latest anime. He then advises her to be on Seiichi's case, since the storyboards for the final episode are not done.
Following her conversation with Aoi, Ema had encountered Yumi while returning to work; Yumi noticed something wrong with Ema and advised her, "Ask, and be a fool for a minute. Ask not, and be a fool for life." In the present day, Midori and Kaori go on a tour across Tokyo. Midori notices Kaori's quick fascination with the city and learns about her dull office life back in the country. Meanwhile, Ema continues to struggle with her cuts, and Sugie continues to try and motivate her, although she does not feel capable of following his suggestions. Elsewhere, the entire production desk discusses what their goals are for the future. While driving over to Kisa's house, Aoi laments about how she seems to be the only one without a dream in mind, then imagines a conversation between her dolls Mimuji and Roro, who have opposing views of the situation.
With production of the other episodes running on schedule, Aoi is put under pressure as Seiichi has yet to finish the storyboards for the final episode. In addition to this problem, there is only one month for the episode's material to be delivered, even if Seiichi finishes early. Also, Musashino Animation president Masato Marukawa, line producer Shun Watanabe, and record producer Gōtarō Katsuragi decide to have the company work on an anime adaptation of a popular book called The Third Aerial Girls Squad. Meanwhile, Misa becomes slightly downhearted at the fact that all she gets to do at her company, Super Media Creations, is model CG wheels. Shizuka manages to land a walla role in a popular anime, but ends up having to hold back her enthusiasm during the recording, much to her dissatisfaction. While having dinner with Misa and Midori, Misa tells them about her own dissatisfaction with work. Watanabe and Katsuragi convince editor-in-chief Tatsuya Hantō to approve of their adaptation, but he adds that he must consult with his superiors. The next day, Misa asks her company's president, Kouichi Tateishi, about if she will be able to work on something other than cars in the future, telling him about her promise to her friends. He advises her to imagine herself in the future first, so she will have an idea on how to reach that goal. Meanwhile, Seiichi feels that he wants to change the ending, so he and Honda meet up with the writer, Shimeji Maitake, who helps Seiichi to reignite his imagination and come up with a new ending that he is satisfied with. However, news of the changed ending puts additional pressure on Aoi, who has to put Seiichi's extravagant ideas into motion.
During the morning assembly, Honda announces that Seiichi will be finished with the storyboards tomorrow, which would still leave the studio with five weeks to deliver the final episode, an unusually short amount of time for such a task to be completed. Later on, Aoi receives an email containing some research about diesel trains from Midori, who had been hoping to help her out on her workload. During a phone call between them, Midori informs Aoi about Misa's situation at work. While delivering a dombra over to the sound department at Sawara Studio for Marukawa, Aoi is forced to help sound effects engineer Toshiyasu Kawano in creating some sound effects for another anime, a process that earns her intrigue. Later, she gets together with the other girls for dinner at her apartment. When Misa contemplates quitting her job, Aoi gives her some advice based on what she learned from Kawano, asking her to figure out where she wants to go before worrying about how to get there.
With a total of thirty cuts to work on, Aoi starts assigning scenes for the final episode to the company's key animators, including Ema at the request of Yumi. However, with dozens of cuts still remaining and not enough animators at Musashino, Aoi struggles to find willing animators working outside the company who would work on the cuts, as other studios are busy with their own anime. She begins contemplating on hiring self-proclaimed amateur animators, but Erika warns her that by doing so, the overall quality of the episode's animation will fluctuate and the schedule will be further delayed due to the director and the animation supervisor having to fix the cuts. While scheduling a meeting with Onodera, a potential candidate, Aoi goes to The Born, an animation company she had previously applied for but was rejected as she did not have a clear idea of what she wanted to do at the time. There, she meets up with Onodera, only to learn that he moved on to become an episode director.
Watanabe, Onoue, Katsuragi, and their playmates discuss about letting Aoi go to Kanno before talking about Musashino's plans to begin work on the anime adaptation for The Third Girls Aerial Squad. Elsewhere, Aoi meets up with Kanno, who, after reading the storyboards, points out the ridiculous nature of animating horses for the final scene and that there are barely any animators left capable of accomplishing such a task. However, he goes on to mention that there is one person at Musashino Animation who is capable of handling the scene. The next night, the staff holds an all-hands meeting, during which Watanabe suggests altering the scene considerably to lessen the amount of work for the key animators. However, Seiichi and Honda protest this, stating that the alterations suggested would ruin the intended tension of the scene. Aoi then relays Kanno's message that Sugie, who everyone had assumed was not suitable for handling scenes for Exodus! and therefore had assigned him to another anime, is more than capable to animating the horse scenes. With the others' approval, Aoi goes to Sugie's house and asks him to take the job, to which he gladly accepts. He talks with the rest of the staff and works out a method that will get the cuts done quickly with help from Ema, Yumi, Rinko, and the other key animators. With the key animation almost complete, Ema tells Aoi that the work has allowed Sugie to still have something to do, then voices that she is now inspired to draw scenes just like he does. Sometime later, Erika returns to work, her family dilemma having been resolved. Sugie approaches Aoi and announces his intention to begin a workshop for key animation at Musashino before thanking her for her work. The delivery day soon arrives, and after everyone works up to the last minute to get the episode delivered on time, it finally airs without a hitch. Aoi, Ema, Tarō, Erika, Seiichi, Honda, Yumi, Ryōsuke, Yūichirō, Rinko, and several other staff members go out to celebrat
At the start of the new year, it is announced that Musashino Animation's next project will be an adaptation of the manga series The Third Aerial Girls Squad. With Honda having just left Musashino and Erika still checking on her hospitalized father, Watanabe assigns Aoi to production manager and Tarō to chief production assistant. Faced with numerous responsibilities and a tough schedule ahead of her, Aoi first starts making sure Seiichi has a clear idea of what he wants to do with the project without making any last-minute changes as he did in Exodus!. When the two ask Rinko to be the series' character designer, she declines the offer as she wants to improve her basic animating skills following her experiences animating the cuts of Exodus! 's final episode. She then recommends Yumi to take her place, and after some reluctance, Yumi agrees to take the job. Next, Aoi and Seiichi talk with art director Yūji Atsumi, who goes into a serious conversation about what kind of clouds should go into the backgrounds in order to fit the scenes. Later, while trying to research on fighter jets for inspiration, Aoi meets up with Midori, who offers to do the research for her and write up an overview of the information. Meanwhile, Shizuka learns that she will be auditioning for The Third Girls Aerial Squad anime, while Yumi and Ema learn some advice from Rinko about the ethics of character design. Elsewhere, Seiichi, Watanabe, Katsuragi, and Shimeji meet with the publisher, but their meeting is finished very quickly when the editor Shinsuke Chazawa approves everything without the author present. Later, as Aoi, Seiichi, and Shimeji do some research, they ask Aoi to have Midori commit to her research on fighter jets while discussing how to go about the ending.
Shizuka shows up for the auditions for The Third Aerial Girls Squad. After reading for one part, she is asked to read for the role of another character. Meanwhile, Aoi and Seiichi once again meet up with Yūji, who agrees to help out with the project after deliberating a question Aoi gave him during their last meeting. Later, a new production assistant, Daisuke Hiraoka, joins the production team. Seiichi participates in a meeting deciding on the cast, with a few members arguing over aspects outside of voice acting and trying to push their own personal choices regarding who should voice the main character. Eventually, the matter is settled by sound producer Yoshikazu Inanami, while Chazawa arrives late and quickly approves of the most popular vote. When it comes to deciding the final character, the one that Shizuka was asked to audition for, Shizuka is considered as a possibility by Seiichi, but in the end, the staff decides to select someone with more experience.
A welcoming party is held for two new production assistants, Tsubaki Andō and Sara Satō, while Marukawa announces that Musashino Animation's reputation depends on the execution of The Third Aerial Girls Squad. Afterwards, Tsubaki and Sara join the rest of the staff as they engage in a meeting discussing the ending of The Third Aerial Girls Squad, then a location hunting trip. Later, Seiichi finishes the storyboards for the first episode, albeit with some dubious drawing quality. Production begins on the episode, with shy key animator Ai Kunogi participating in her first production meeting, where she is assigned by Seiichi to animate a scene.
Aoi informs everyone to stop production on the characters, despite there being only three months until the first episode airs. Yumi begins revising the character designs based on the author's feedback emails. However, she struggles after Nogame voices his disapproval of the redesigns and gives out vague feedback. With an actual meeting with Nogame impossible, Watanabe advises they should start from the beginning again without anything to go on. After Aoi speaks with Yumi at her secret spot in the local park, she and Seiichi focus on the unaffected material outside of the characters, such as the 3D and backgrounds. Seiichi stresses to Yūichirō and Yuuji the importance of emotions over realism, later telling Aoi his advice was inspired by his experiences after the release of Jiggly Jiggly Heaven.
The anime adaptation for The Third Girls Aerial Squad is announced to the public, but it is met with skepticism from the otaku community. Honda decides to pay a visit to the studio to share some cakes and catch up with everyone, surprising the staff with his drastic weight loss. Later on, Aoi and Seiichi hold an art meeting with Yūji and decide to hire another art director named Masahiro Ōkura to handle the background scenes. Meanwhile, the studio is suddenly pushed by Chazawa to create a promotional video in two weeks for a Manga Festival event, meaning certain cuts need to be fully animated quickly. Tsubaki and Sara handle their workloads with varied results, while Sugie notes to Ema her close relationship with Ai. While Misa finds out her specialty in creating CG wheels, Shizuka fills in at a children's stage play when the costume actor goes missing, managing to handle both movement and voice acting at the same time.
Aoi, Seiichi, and Katsuragi join Inanami as they meet up with the voice cast of The Third Girls Aerial Squad for a recording. During the recording session, the staff notices the protagonist's voice actress, newcomer Kyōko Suzuki, is struggling with maintaining the quality of her voice as they expected her to do. They later help her give a more natural performance. Afterwards, Aoi meets up with Ōkura at a bar to ask for his help with a particular background; exhausted and drunk, he hastily agrees to do it. Aoi then contacts Studio Taitanic about the layouts of the fifth episode, only to learn they are halfway done despite having not been sent over to Musashino. Later on, when Aoi and Yuuji visit Ōkura the next day, he initially turns down the offer, having forgotten about his meeting with Aoi and being disillusioned with the use of 3D animation over 2D animation. He only changes his mind when Aoi relays a message to him from Marukawa, about his pleasure of working with him. Later on, Musashino receives the layouts for the fifth episode, but the staff is forced to have an urgent meeting with Studio Taitanic's Zaruyoshi Yakushiji, the episode director, over several errors on the layouts that he let slip by. He begrudgingly agrees to check the errors, but insults Seiichi while leaving. Aoi later learns that Yakushiji suddenly quit the job. Needing to find a replacement director, she begins to stress out until Erika makes a surprise return to the studio.
On the rooftop of Musashino Animation's studio, Aoi pleads with Erika to take her job as production desk and then blames herself for the problems happening lately. Erika then advises Aoi to go home for the night and get some rest so she can get rid of her stress by the next morning. The next day, as Aoi, Watanabe, and the entire production desk discuss how to handle the issues with Studio Taitanic, Erika goes with Hiraoka, who is actually a former acquaintance of hers, over to Taitanic's office so they could help out with the fifth episode. Eventually, she selects Hiroshi Iketani as Yakushiji's replacement. Meanwhile, Marukawa takes Aoi to the offices of the bankrupt Musashino Pictures studio, which produced Aoi's favorite anime Andes Chucky, much to her own surprise.
As the head staff tries to discuss what to do for the plot of the thirteenth episode, they start to liken the protagonist's reason for flying to their own reasons for getting into the anime industry. They become interested by their motives for making anime and ask the rest of the staff for their own opinions, receiving various responses. Meanwhile, Midori, who has been given writing assignments by Maitake to improve her writing skills in lieu of directly teaching her, feels downhearted when an increasingly irritable Hiraoka implies that she can get her way just because she is a girl. She talks about it with Maitake, who assures her that his reasons for giving her the assignments were work-related. Later, after the production staff comes up with a scenario for Maitake to work on, Hiraoka gets into a heated argument with episode director Hironori Madoka, who feels the key animators provided by Hiraoka from Studio Taitanic have been of poor quality.
During a delivery by the president of A.C Tsuchinoko, Hisamitsu Isokawa, he reunites with Hiraoka and Erika, who were his classmates in technical school. Meanwhile, Misa gets the chance to do some character CG animation for a certain scene in The Third Aerial Girls Squad, inviting Ema and Shizuka to an amusement park to observe their reactions on a rollercoaster for inspiration. Following the successful premiere of The Third Aerial Girls Squad 's first episode, which is met with widespread public acclaim, Aoi receives complaints from Segawa, who requests that Hiraoka be taken off the episodes she is working on due to the lack of quality in both his key animators and his attitude. When Aoi relays this to Hiraoka, he becomes angry, stating that fussing over quality just makes his job harder.
After being assigned as the animation supervisor for the thirteenth episode, Yumi, pressed by her large workload, nominates Ema to join Rinko as an assistant general animation supervisor to help her handle some of the cuts, having been impressed by the progress she displayed since Exodus!. However, when Aoi asks her about it, Ema responds that she lacks confidence in herself to take up the job and has to think it over. As a backup plan, Aoi approaches Segawa with the request. Though she declines, Segawa becomes impressed be her sincerity and regains some of the motivation she lost following her incident with Hiraoka, returning to work on the twelfth episode. Meanwhile, Ema checks on Midori and finds that she is enjoying her job in script ordering. Later that evening, as Nao Shinkawa drinks over her troubles alongside in-between animation inspector Chiemi Dōmoto, Hiraoka shares with Tarō about how his horrible experiences during previous jobs left him with a cold attitude towards the anime industry. Meanwhile, Misa comes over to the studio to get some advice from Ema on how to improve her CG animation. She eventually manages to improve it greatly by incorporating 2D animation techniques into the mix. The next day, Ema receives encouragement from Sugie and decides to take up the assistant supervisor position. Afterwards, she relays her confidence to her mother, which in turn gives Ai the confidence to attend a meeting by herself. Meanwhile, just as recording wraps up on the final episode, Katsuragi is shocked to learn that Nogame has rejected all of the last episode's storyboards.
After Watanabe and Katsuragi fail to convince Chazawa and his boss to let them contact Nogame and negotiate with him, the Musashino staff is left with no choice but to follow his wishes and keep the episode's plot accurate to the story's original timeline, which would end the anime on an unhappy note with the death of one of the main characters. However, Seiichi is unsatisfied with the prospect, feeling that the ending needed to be positive. Hiraoka reveals that he worked on an adaptation of another of Nogame's works, which ignored the original story and sparked significant backlash from the fanbase. Encouraged by Marukawa and Honda, Seiichi finds Nogame's email address and manages to arrange a meeting with him in person.
With three weeks left until the delivery of the final episode, the entire Musashino staff reinforces their efforts to get the episode done with the time they have left. The work is particularly focused on the scene featuring Shizuka's character, which is assigned to Ema at her own request after she was touched by Shizuka's performance. Meanwhile, Shizuka finds enjoyment in being able to land minor voicing roles, while Misa stays up the entire night at her workplace creating a CG model for a fighter jet. On the day of the delivery, after the episode is finally completed, the production staff is tasked with delivering the final tapes to the various TV stations across the country in time for the airing by any means necessary. As the others reach their assigned destinations in time, Aoi is held up by several transport delays and is forced to complete the remainder of her trip by running to her destination on foot.