Moritaka Mashiro, an average student with a talent for drawing, forgets his notebook at school, where his classmate Akito Takagi finds and looks through it. Takagi likes his drawings and asks Mashiro to team up with him to create a best-selling manga. Mashiro refuses because his uncle was a manga artist until he died from overworking, while deeply in debt, which derails his dream. Takagi soon invites him to visit Miho Azuki, the girl Mashiro has an unrequited crush on, and Takagi tells her of his plan to create a manga that will become an anime, in which she will play the heroine. Mashiro also proposes to marry Azuki when both their dreams come true, and she agrees that they will, but shall not see each other until then. With this motivation, Mashiro decides to become a manga artist.

Mashiro chats with Takagi, who tells him that he chose Mashiro because he is smarter than many of his peers in matters outside of scholarship, and that he believes Azuki has a similar kind of intelligence, with the ability to be appealing to others. Mashiro tells Takagi that he believes his uncle committed suicide, and thus suspects that his parents will oppose him becoming a manga artist. Mashiro's mother says his uncle did not commit suicide, but still opposes his decision until his father and grandfather show support for his dream. Mashiro's grandfather gives him his deceased uncle's studio apartment, and Mashiro brings Takagi to see it.

Mashiro and Takagi arrive at Mashiro's uncle's apartment, where they look around and Mashiro shows Takagi the manuscripts and storyboards, that the author of a manga series produces before drawing it. Mashiro realizes that his uncle was working extremely hard until his death and vows to approach it with the same resolve. Mashiro and Takagi find letters between his uncle and his friend from childhood, which stop before his hit manga was serialized, and looking at a yearbook photo of her, realize that he had been in love with Azuki's mother. They go to visit Azuki's mother the next day, and learn that she was also in love with him, but never could admit it and fell in love with someone else. Mashiro asks Azuki's mother not to tell her about the relationship between her and his uncle, and he then sets out to make a manga.

Mashiro shows Takagi all that he has drawn and points out all the mistakes he has made, as well as the finer points of using tools for drawing manga. When Takagi questions him, Mashiro tells him about G-Pens and Kabura pens, making manuscripts, and Taro Kawaguchi's three rules to a successful manga: conceit, doing your best, and luck. When they go to a convenience store, Takagi notices that the latest issue of Jack has a semi-finalist named Eiji Nizuma, a fifteen year old manga creator. The two discuss their high schools, manga, and editors, thus coming to the conclusion that they would finish the manuscript for a manga by summer's end and show it to an editor of Jack. While walking home with Takagi, Mashiro encounters Azuki by chance; while the two are unable to look at each other as they pass, they both turn back to look.

Mashiro starts work as an assistant for Nizuma, and meets the other two assistants; Shinta Fukuda, who had placed lower than he did in NEXT, and Takurō Nakai, who won an award 10 years ago, but has been unable to accomplish anything noteworthy since then. Despite Fukuda and Nizuma questioning why he is working as an assistant instead of trying to get published, Mashiro is determined to learn what he can to help Takagi. Fukuda realizes that "Crow" will eventually get canceled after the novelty wears off if Nizuma does not make it more substantial and interesting. Nizuma adjusts the story accordingly, while also deciding to meet with his editor.

The story picks up directly where the Season 1 finale episode left, introducing Miura as Moritaka and Takagi's new editor and introducing the genius, yet extremely lazy ex-salary man, Hiramaru at the New Year's Party.