The series follows talented artist Moritaka Mashiro and aspiring writer Akito Takagi, two ninth grade boys who wish to become mangaka.
Takagi and Shiratori's manga Rabuta & Peace is entered into the serialization committee and it is published in the November issue of Shonen Jack placing 5th in the voting charts. Mashiro decides to use his free time to improve his drawing skill, aiming to reach a level where he can draw two manga simultaneously and be on par with Niizuma. Shiratori's mother disapproves of him drawing manga because of their family's high class reputation causing him to run away from home. His family then comes to the studio looking for him where Shiratori's mother insults everyone there by looking down on their manga artists' abilities. This leads to a heated exchange of words by both parties. Hiramaru and Aoki's serializations are both canceled due to low ratings and enter into an upcoming competition, Super Leaders Fest. Upon learning of this and Niizuma's participation (meaning that he will now be working on three manga) Mashiro decides to enter on his own with a new manga, since he doesn't want to affect Takagi's quality on PCP and Rabuta & Peace. However Takagi states that they will enter together.
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.
The results of the serialization meetings are announced and everyone finds out Niizuma is the one who did the art on +Natural.
Azuki and Mashiro continue to fight with each other over trust. Takagi and Miyoshi both feel extremely guilty, and blame themselves for them fighting. Takagi finally decides to explain what happened to Miyoshi, considering Mashiro and Azuki are too stubborn to apologize to each other. After planning to meet at the zoo, Takagi is met by a crying Aoki, who hugs him, causing Miyoshi to run off. When Takagi finally reaches her, he proposes to her. After a talk with Aoki, they decide to get married after he gets serialized. They invite Azuki to tea, and Azuki forgives Mashiro, much to his confusion.
Takagi comes up with some more ideas, including One Hundred Millionth, a story about people being ranked according to their abilities, and Hattori is impressed with the story, causing Mashiro to wonder if his art is good enough. The story is chosen as one of the finalists, but does not make it to the four chosen for the award or honorable mentions. Shortly afterward, Ishizawa, a classmate, claims that Mashiro's art is holding Takagi down. Takagi gets angry and punches Ishizawa.
"Perfect Crime Club" gets rave reviews, but the serialization committee must decide if it can beat "Crow" and "+Natural."
In an effort to motivate them, Hattori snubs Ashirogi Muto at the Christmas party. +Natural is released to critical acclaim, but Tanto is holding steady.
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 appealling 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.
Recalling when he and Azuki turned back to look at each other at the same time, Mashiro tells Takagi that he and Azuki have been on the same frequency for years, indicating that they are connected without having to say anything about it. Azuki's best friend Kaya Miyoshi goes to Takagi to complain about him telling Azuki about her dream, and as she does so, gives indications of romantic interest in Takagi that Mashiro and Miyoshi notice. During the summer, Mashiro and Takagi stay at Mashiro's uncle's office, and work on a manga called The Two Earths. When it is complete, they call the Shonen Jack editorial department.
Mashiro, at Miyoshi's suggestion, sends an email to Azuki to begin correspondence with her. During the first day of high school, Mashiro and Takagi submit their new pseudonym, "Muto Ashirogi". Hattori is impressed with their work, but Mashiro notices that he is not expecting Money and Intelligence to be serialized, wondering if it is because of his desire that they wait until after high school to get serialized. Money And Intelligence gets first place in the early results of the NEXT polls, but drops to third place in the actual results, with Nizuma's work getting half the votes. This development convinces Mashiro and Takagi that they must make a mainstream work to go for first place, and resolve to make one better than their previous efforts.
Trap resumes publication, but is cancelled due to low rankings.
The boy's new gag manga is published in NEXT, however both have serious problems in their love lives.
Mashiro and Takagi meet with Akira Hattori, one of the editors at Shonen Jack. He notes that their work has flaws, as it is too text-driven and not drawn in manga style, but they have potential. He tells them that they are better suited to figuring out what could be a hit and drawing that, rather than drawing what they want, and while they are less likely to get a smash hit with that skillset, they are more likely to follow up on one if they do. Hattori gives them his contact information, encouraging them to come to him with their work. At school, the teacher decides to seat boys and girls next to each other, resulting in Mashiro sitting next to Azuki.
Miura's data research concludes that the team should focus on a gag manga, however Mashiro and Takagi are not so sure.
Nakai vows to do whatever it takes to renew his partnership with Aoki.
The team begin on their new anime, a reworking of "Money and Intelligence." When the serialization committee rejects it, Miura suggests they try mainstream fantasy.
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, realized 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 her uncle, and he then sets out to make a manga.
The serialization committee decides to serialize Aoki's What God Gave Me and Nanamine's What You Need for a Meaningful School Life. As Kosugi begins to be bothered by Nanamine's method, Hattori senses his discomfort and visits Mashiro and Takagi to gain some insight on Kosugi's attitude, which they reveal is due to Nanamine's unorthodox method, enraging Hattori. At the same time, Nanamine calls Akito to gloat about his serialization, but Ashirogi Muto states they will crush his methods using all the hard work they have put into PCP. Unperturbed, Nanamine says that they will let the rankings decide who is superior. Eventually, Hattori confronts Kosugi and is able to lift his spirits by reminding him of his value as an editor. As Nanamine collaborates with his internet acquaintances, some drop out after becoming fearful of his intention to challenge Ashirogi Muto. While Mashiro and Takagi decide how best to contest Nanamine, they realize, that they can best counterattack, by pitting the climax of PCP's current arc against Nanamine's second chapter. Eventually, as Kosugi reviews Nanamine's work and points out the weakness in his background drawings, Nanamine reveals his secret weapon: a returning Takuro Nakai.
The team awaits the results of the serialization meeting. Nakai considers quitting manga and returning home. Hattori talks to Nizuma about doing the artwork for a new project.
Hattori goes over the weaknesses of Mashiro and Takagi's storyboard, and tells them that they need good characters, simple yet exciting battles, cute heroines, and tragedy and humor to make a good storyboard. Nizuma admits that he wrote the name on the spot, rather than having it in his head, and Mashiro and Takagi realize that he is a "genius" who can draw what he wants. Nizuma tells his editor that he likes the passion in Mashiro and Takagi's eyes, and sees them as his rivals. Meanwhile, Azuki auditions for Saint Visual Girls' Academy, a midnight anime, and gets a bit part. Mashiro, seeing her progressing toward her dream, becomes somewhat impatient and asks her to continue waiting for him, and she promises to do so while telling him to stop sending emails like that.
Mashiro and Takagi both decide to rewrite their manga. Fukuda, Aoki and Nakai also rewrite their manga. Later Fukuda's manga is shown first with positive reviews. Next Mashiro and Takagi's manga is also shown with good reviews. Nakai panics and thinks that when Nizuma said that the winners were tied and there was a third place, he meant his manga. Then Aoki and Nakai's manga is shown with also positive reviews. All three series are okayed to begin work on names for serialization. Azuki said that she liked Mashiro and Takagi's manga, which gives Mashiro hope.
Feeling they will never beat Niizuma with their current manga, Ashirogi Muto consider quitting Tanto.
The team's newest work "Stopper of Magma" is rejected without consideration for serialization. Miura reveals he has been receiving advice from Hattori, who suggests they draw a serious comedy. Muto Ashirogi follow Hattori for inspiration, and develop the idea for their last chance manga.
The committee decides the fate of "Perfect Crime Club," and the team gets a new editor.
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.
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