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.

Mashiro and Takagi get to know their new assistants, while Azuki struggles with her decision to do an ecchi photo shoot which will boost her popularity a lot. When Mashiro receives an e-mail from Azuki, he is left shocked by what she's decided; if he's okay with it, she wants him to see her naked first so he won't mind if photos of her in a swimsuit are taken. Worried, Mashiro neglects his storyboard to go visit her and talk things through. Takagi calls her and explains what's happening. Shocked to hear what Mashiro is about to do, she finally contacts him to talk about it and he tells her he doesn't want her to do the photo shoot. They decide to go to the beach some day and take photos themselves.

Nakai vows to do whatever it takes to renew his partnership with Aoki, showing his determination to an extreme extent, worrying Mashiro, Fukuda and the rest.

As TRAP's ranking continues dropping, Mashiro and Takagi consider some major changes. In the end Miura tells them they do not have to resort to drastic changes, they should focus on continuing a real detective manga instead. Takagi wants to protest but Mashiro convinces him and tells him he thinks it's their best chance to get better in the rankings too.

Their earlier decision pays off as TRAP begins to move in the rankings, but the competition gets very fierce. Overwork is slowly taking its toll on Mashiro, especially when he is asked to draw a colored page for their first manga volume promotion.

In the end Mashiro faints and is hospitalized, but he refuses to stop drawing even in his current condition. Despite Mashiro and Takagi's wish to continue, TRAP is put on hiatus. Azuki visits Mashiro in the hospital. She talks about how she liked him ever since she was a child and they talks about a special day at the pool during middle school. While Mashiro is convinced he can continue to draw, but Takagi is hesitating because of his current condition. In the end, Azuki is the one who supports Mashiro to do what he really wants to do, surprising Takagi and Miura by her decision.

The chief editor decides to put "TRAP" on hiatus until Mashiro and Takagi's graduation. He decided to do so because of Mashiro's uncle, whom many thought to have died from overworking himself, as he does not want the past to repeat itself. As the editors hear of the hiatus and reason why, most disagree with the idea but figure they can't do much about it. When Fukuda hears of the reason he gets furious and begins a boycott, including Nizuma, Hirumaru and the Aoki & Nakai team. They all decide to put their work on hiatus too until TRAP will be published again.

The boycott is still in full effect but the chief editor hasn't changed his mind. Meanwhile Mashiro and Azuki continue their still awkward yet happy meetings in the hospital. Seeing how hard Mashiro and Takagi work, Miura makes one last desperate plea to sway the chief into resuming TRAP but he ultimately fails. In the end Mashiro and Takagi show the chief the work they have done so far, managing to convince him with their guts.

In the end TRAP resumes publication, but is struggling with low rankings. Takagi tries to put some ideas based on fan mails in the name but Miura tells him he can't use whatever idea and add it to the story, because then it wouldn't be their manga anymore. Meanwhile, Azuki gets more and more popular, getting a semi-regular role in an anime. In the end TRAP is ultimately cancelled due to the low rankings, together with Aoki's & Nakai's Hideout Door. Mashiro and Takagi finish TRAP and are frustrated they weren't able to do better and realize they won't be able to get an anime before they're 18. Mashiro tells Azuki about this and she tells him she'll wait for him forever but would like to get married by the time she's 40. Not wanting to make Azuki wait that long, Mashiro and Takagi get fired up again to do their best with their next manga.

The team must decide which genre to choose for their new manga. Miura urges them to draw a gag manga, but Mashiro and Takagi aren't sure they're fit for gag manga and prefer something more serious which is their forte. In the end they decide to create 2 new one-shots, one funny one to Miura's liking and one more serieus one, more to their liking. They show both Hitman 10 and Future Watch to Miura who tells them to try to get Hitman 10 serialized. This causes Mashiro to feel like this editor really is a "miss" since according to him, Future Watch is a lot better. In the end it's revealed Ashirogi Muto submitted Future Watch behind his back in the newbie contest, the Monthly Awards, in order to get all the editors, higher-ups and especially the manga artist judge, Niizuma, to read it.

Both Ashirogi Mutos' one shots Future Watch and Hitman 10 are well received by the editorial staff. The chief decides to run both as one-shots, wanting to see the public reaction before making a decision on a possible serialization. Mashiro and Takagi aren't sure about their new editor and his skills and this gets worse when Takahama calls them because his manga Business Boy Kenichi ranked 6th as serie while it got 2nd place as one-shot, telling them not to listen to Miura too much and do things in their won style because taking Miura's advise made him fall down in the rankings. In the end Hitman 10 ranks 10th, while Future Watch ranks 9th.

Miura's data research concludes that the team should focus on a gag manga because they're steadier in the rankings but Mashiro and Takagi are still not sure about it, especially Mashiro. During a meeting Miura pushes them to do it while Mashiro keeps declining the idea, stating gag doesn't suit Takagi's writing style and his art style at all. Miura tells him he shouldn't decide things on his own, since Takagi isn't really against the idea, and tells Mashiro to work on his artstyle or to let Takagi have another artist do the artwork. Upon hearing this Takagi snaps and tell Miura "they can't work with someone like him" and both of them leave. While on their way to the studio, Mashiro tells Takagi he doesn't mind doing a gag manga as much but he was happy Takagi defended him. Later that evening they receive several boxes Miura sent earlier, containting material about gag manga, and Mashiro and Takagi realize how passionate Miura is about gag manga. When he comes over to apologize they tell him it'd be fine to do a gag manga.

After confirming to do a gag manga with Miura, Takagi goes to the zoo to get some inspiration for his next heroine. There he meets Aoki and they decide to exchange information about the way guys and girls think and experience things, helping each other out as fellow manga artists. Because of their constant phone calls, Miyoshi always gets the "busy signal" when she tries to call Takagi, making het a little suspicious. After Aoki, Takagi, and Iwase all meet at the zoo, Takagi receives a book from Iwase which she wrote herself. When Takagi isn't upset about her winning a prize and refuses to compare his work with hers, she angrily declares she will become a manga story writer as well. When Miyoshi finds Iwase's novel at the studio and a hidden letter inside, she leaves the office in tears.

Mashiro and Takagi finish their manuscript and submit it to NEXT. Miyoshi is still thinking about what happened, and decides to call Azuki, who in turn decides to call Takagi. After Takagi fails to explain what really is going on, she attempts to get more information out of Mashiro. After questioning Mashiro on whether or not he has been honest with her, she hangs up, leaving Mashiro thinking he has been dumped.

Takagi and Miyoshi blame themselves over the fact their fight has caused a rift between Mashiro and Azuki. Because Mashiro and Azuki are too stubborn to apologize to one another, Takagi decides to explain everything to Miyoshi at the zoo. The meeting is complicated when Takagi runs into an upset Aoki just as Miyoshi arrives. In an effort to get Miyoshi to stay, Takagi proposes to her and she accepts after Aoki explains everything. In the end Miyoshi allows Takahi and Aoki to keep contact at the condition she and Aoki will become friends too. They invite Azuki to tea and she mails Madshiro that she forgives him, much to his confusion.

Aoki asks Nakai to draw the art for her new manga but he states he only will on the condition she will go out with him, angering her to the point she slaps him. Afterwards she continues her in search for someone to help her draw sufficient panty shots in order for her manga to have a more "shōnen" feel to it, but isn't able to find anyone suitable. After many events, Fukuda ends up offering his help, since his manga Kiyoshi Knight is doing so well due to his own well-drawn panty shots. Aoki is hesitant to accept his help but under the circumstances she has little choice but to accept it in the end.

Takagi and Mashiro's new manga Tanto doesn't get serialized but Miura tells them they just have to make it better for the next meeting. "Business Boy Kenichi" gets canceled, leaving Nakai jobless. After being rejected twice he reflects on his behavior and decides to go back home. Mashiro tries to stop him but Nakai won't budge, not even when Fukuda and Aoki show up. Later, Takamara asks for a different editor because Miura won't let him draw what he wants but the chief editor refuses, saying that if his work is good enough, the editor will be forced to accept it, making Takagi and Mashiro realize the same thing. Niizuma becomes the artist for Aiko Iwase's manuscript while promising he'll continue CROW and not let the quality drop, thoguh he states he'll only do it on the condition it'll be serialized, which Hattori (who will be the editor of the new manga) is confident about. Worried how the higher ups will react about Niizuma running two series, Hattori asks him to change the art style a bit and use a pen name until it passes the committee.

Miura gets worried when he hears the positive reactions about the "newbie" manga artist who drew the storyboard for MONEY's. Takagi and Mashiro find out that Aiko Iwase is the story writer, fueling their competitive feelings. Aiko pays Takagi a visit, asking him to acknowledge her if she ends up being more popular, which he promises but only talent wise. He tells her he and Miyoshi are engaged. The committee finds out about Niizuma being the artist for MONEY's but can't deny its quality. In the end Hirameki Tanto-kun finally gets serialized but Niizuma's new manga +Natural does so as well. Takagi also gets invited to Miyoshi's house regarding her parents approval for their marriage. As Team Fukuda hears about Niizuma's double serialization they have a meeting with a short interruptance of Iwase. When they visit Niizuma and ask him why he took up the job of the second manga, Niizuma declares he draws because he wants to and no one is allowed to whine about it until they make a better manga, reverting to his normal self afterwards.

Takagi goes to Miyoshi's house to announce their engagement to her parents. The two families have surprising connection and everything goes well between them. Later, the pair attends a party where Niizuma's second series motivates them as rivals. Takagi is feeling more and more pressure as Otters, Hiramaru's manga, gets an anime series. Tanto's release follows that of +Natural (Iwase and Niizuma's new manga), and to their disappointment, it does not beat +Natural's second chapter in the rankings. Iwase suddenly claims she has a crush on Hattori and out of the blue, Niizuma announces he's not reading Ashirogi Muto's manga anymore...

It's time for Takagi and Miyoshi's wedding. Mashiro is still unsure if Tanto fits their style and ends up arguing with Hattori, who refuses to give his opinion about their manga. In the end Mashiro gets Hattori to admit he thinks their manga isn't good but he also tells him he still thinks they can beat Niizuma. When Niizuma declares on tv that Ashirogi Muto is his number one rival, Mashiro has a break down. He runs home and calls Azuki, saying he wants to quit Tanto because he wants to aim higher, because he wants to compete with Niizuma. Mashiro talks about it with Takagi and they decide to quit Tanto. The chief editor tells them to quit the company if they behave like this but Mashiro states his wish to beat Niizuma but that he's unable to do so with Tanto. The chief asks Takagi if he thinks they can beat Niizuma with a different work, so Takagi declares they'll submit something to the following 3 serialization meetings that can compete with Niizuma's work. If they fail to do so, their contract will be terminated.

Mashiro and Takagi try hard to come up with good names for their new serie. Miura tells them they should work on a serious darker manga, like Money and Intelligence, so they decide to create an edited and more complicated version of their earlier manga, naming it Money, Intelligence and Appearance (aka KTM) which is also incredibly deep. However, it is not accepted for serialization. For the next meeting they are pushed by Miura to seriously attempt writing a mainstream fantasy manga with a simple setting, unlike TKM, against their own ideas. While they feel a "standard battle manga" isn't working for them, Miyoshi states the manga is enjoyable and that the simple setting is good for a change. In the end that manga gets rejected too, leaving them with one last chance.

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.

Editor Oonishi, changes his vote to be positive, stating it's ridiculous to let Ashirogi Muto go because of this voting. The vice chief editor also changes his vote, stating they should leave it up to the readers to decide this matter. In the end the manga gets serialized. Mashiro, Takagi and Miyoshi receive the good news and eat home made cake from Azuki. They find a USB in the cake and listen to her special recorded Christmas carol. Mashiro and Takagi's editor changes again but it turns out to be Hattori, while Miura becomes the editor for +Natural. Hattori tells them about the initial voting result, triggering a brainstorm session where they discuss what they should change to make the manga even better. Hattori thinks it's Niizuma's 'expressiveness' that makes his manga so good but Mashiro changes it to 'imagination'. Mashiro decides to, just like Niizuma, draw the manga based on only Takagi's script (instead of his storyboards), giving him more freedom to draw the panels as he wants. Both of them start to rewrite the storyboard. Meanwhile Fukuda tells his editor he's working on a one shot, saying he doesn't want to lose against Niizuma and Ashirogi Muto.

Mashiro changes the character design while Takagi struggles with naming the 3 characters and a possible new title. Orihara comes back as assistant + 2 new ones: Moriya and Shiratori. Those 2 argue if sales or treating it like an art is better for a manga. Mashiro tells them he and Takagi draw with sales in their minds, because they're not yet good enough to draw something that has true cultural value, saying that everyone should draw the way they want to. Takagi decides on the title; "Perfect Crime Party", aka "PCP". Meanwhile Fukuda is working on Road Racer Buchigiri. Everyone is curious how the votes will be with PCP as a story based manga against the intense and flashy Road Racer. In the end "Perfect Crime Party" gets 1st place and gets a total of 422 votes, amazing the editors because CROW "only" got 401 and +Natural 310 votes on their first chapter. The achievement is especially good since CROW didn't have a one shot like Road Racer to compete with at the time. Fukuda's Road Racer gets serialized too. Hearing +Natural dropped to the 8th place, Iwase gets fired up, as does Niizuma. At the end Mashiro, Takagi and Hattori visit Mashiro uncle's grave. Mashiro tells him he finally got 1st place and we see his uncle 'answering' that it should be a given and that when he truly becomes number one, he should come back again, but he smiles proudly.