While Bossun and the Sket Dance are helping the basketball team due to Jogasaki's little accident, Saaya works up the courage to confess to Bossun. Meanwhile, Sojiro thinks Saaya is still in love with Tsubaki. Can Bossun and the gang help the basketball team and what will happen between Saaya's undying love and Bossun?
When class 2-D's Shuuichi Morita loses control, Kiri's action makes him throw the chair towards Mimori. Sasuke tells Kiri to cooperate, but Kiri refuses to follow Sasuke's orders. Later, Himeko hangs out with Kiri who shares his story about Kihara who was a victim of Kutsuwa, a teacher from his old middle school. When Kiri's old teacher comes back to Kaimei High School and bullies Himeko, Kiri Kato loses his composure.
After Hime discovers a peeping tom who stare at her as she changed in the girls' locker room, she asks Bossun and Switch to help catch the creep. However, Bossun and Switch ignore her plea as they watch a student spider climbing. Meanwhile, Roman and Michinori are having a manga face off to determine who is the better mangaka.
Sasuke is selected to be the new president of student council replacing Sōjirō. For his goal of making Kaimei High a better school, he becomes strict about everything that deviated from school rules. But in the end Sōjirō has to tell him that there are more important things than rules. Three days later, Sasuke officially replaces Sōjirō. In his speech, he says he will make Kaimei High a better school with everyone's co-operation, this gets a big applause.
Bossun wants to poop so bad. But he faces many troubles from the toilets he wants to use, like the school toilet's being broken (thanks to Dante), a convenience store's toilet being investigated by the police so Bossun can't use it (thanks to a robber), forgetting his home key, mistaking his home for a woman's and ending up presumed a pervert (his trousers undone when the door opened).
Tsubaki shows off his lame t-shirt, and his student council members are not looking forward to it. Sojiro promises Tsubaki that he will wear his t-shirt if it's stylish. Tsubaki heads over to asks Bossun for his artistic advice. Meanwhile, Switch and Bossun are evenly matched in their quiz challenge on a popular mecha anime show, Code A: Chian's Counterattack. Switch invites Bossun to a meeting between the otaku to see who is best between him and Switch.
The Sket Dan trio discovers that Hosuke is sick of his food that Saaya usually gives him (Sausages), by arranging the Sausages into Katakana, saying it is wanted to eat something else. Switch later uncovers another weird invention that could translate an animal's thoughts to human language in a 1-5 meter radius. However, it works but not only for Hosuke, but their (Bossun, Himeko, Switch, and a certain girl) inner thoughts also are translated.
While Saaya is talking to Sasuke and says she's interested with Sasuke and Bossun's relationship, the council members Daisy, Mimori, and Michiru hear and get the wrong idea, thinking they are interested in each other. Michiru tells Sojiro about this. When he asked Saaya if she's interested in someone, she gives Bossun's details which Sojiro misinterprets as Sasuke's, getting the wrong idea.
Switch attempts to prevent Saaya from talking to Bossun, but Reiko and Sasuke distracts him. When Saaya gets to Bossun, Switch decided to not interfere with the two's feelings. Saaya finally asked Bossun (Himeko) how he feels about Himeko. She had never thought about it before, but answered like she's Bossun. Later that night, Himeko explains to Bossun about Saaya's question. What did Himeko said to Saaya?
Due to Bossun and Himeko's situation, things get tense when their female classmates asks Himeko (Bossun) to change or to take a bath, and Bossun (Himeko)'s help is making things worse. Meanwhile, Switch is keeping an eye out for Saaya, Sasuke is acting like a cat, and Chuma is making a cure for Bossun and Himeko. Can Bossun and Himeko avoid giving out secrets during their ski trip?
Himeko gets a chance to star in Pelocan's latest TV commercial as the proud Pelocan girl. Despite being a devout fan who knows every Pelocan candy flavor by heart, she has stage fright. Later, Hime has her Sket Dan crew have a study session at her house because they have the dreaded practice exams. However, Hime and her friends are easily distracted.
Bossun gets addicted to his phone when Shinzo makes him exchange e-mails with the manager of the Sengoku website, Pudding. As he responds back and forth, he gets hooked on. At the same time, Himeko also gets a pen pal when she fills in for Koma to help reply to Samurai. As the two get close with their pen pals, they arrange a date to meet each other.
The Sket Dan get a request from Saaya, a girl who looks and acts like something right out of a dating sim game. She wants to try and get rid of her tsundere tendencies toward boys, and so starts coming to the clubroom everyday in an attempt to become comfortable speaking with the opposite sex. Later, Saaya finds an abandoned pet owl in the park and the Sket Dan end up caring for it in their clubroom. Owls are supposed to be carnivorous and hard to raise, but... this one is almost ridiculously tame.
Funzō thanks Bossun for helping his sons and does a super rolling grovel out of the window. In the maid cafe, Funzō makes an order to Moe with his sons. Then, Akane and Rumi arrive to the maid cafe. Akane marvels about how beautiful Himeko has become. Rumi asks Switch about Bossun's relationship with Himeko and wonders if Bossun will be after his little sister. Switch replies that they are friends and assures her that Bossun would never go after Rumi that way. Outside, Dr. Tsubaki finds Bossun, and he begins apologizing to Bossun once he and Bossun are on the roof. When Dr. Tsubaki states that there is someone who shares his blood, Bossun recalls his father's letter. He realizes that he has a twin brother. Dr. Tsubaki states that he has harboring this secret for 17 years and says that his son had already found out. Bossun thinks back hard and realizes that Sasuke is his twin brother. Meanwhile, Sōjirō and his student council group wonder where Sasuke is.
Angry at the world and surrounded by loneliness, Bossun finds himself at the place where his father was slain in a car accident. A young man appears and explains to Bossun why his father died. He gives Bossun, a letter and present from his father that was supposed to be given to Haru. When Bossun sees a young man bullied by delinquents, will Bossun follow his father's philosophy or will he just live for himself?
It starts with man who looks like Bossun, yet viewers find out that he is Ryōsuke, Bossun's father. In the present, Bossun recalls finding old tapes and learns about his father. When Akane comes home, she finds Bossun watching the tapes, so she quickly locks them up. Desperate to know the truth, Bossun goes through the photo albums. What did Bossun uncover about his father and Akane's secret?
After Switch fixes Yamanobe's Fancy Yunpyouter, Yamanobe has the Sket Dan crew play a game called Special Broken Mariko which is the parody of Super Mario Brothers. (See Special Mariko Broken page) Later, the Sket club and the rest of the cast celebrate the New Year with a compilation of clips from the anime.
After being betrayed by Arisa, Himeko transfers to another school to start a new life, but the rumors of Onihime still prevails. When Himeko knocks out a softball far during sports, Chiaki tries to convince her to join the team. Even though Himeko declines Chiaki's offer, she warms up to Chiaki and eventually to Bossun. When Chiaki gets bullied by some thugs, Himeko struggles to choose between saving Chiaki and risk exposing her Onihime side or not.
Himeko breaks her Cyclone while helping a client who was being assaulted for some cash from a bully. Because of that, she has to buy a new field hockey stick. As she bought one, she's reminded of her past before she met Bossun and Switch. As a result, Hime goes to a high school named Kaimei Academy where she meets Captain and Bossun.
Bossun and his gang take a mission to rescue Roman, but the mission goes awry when Bossun and his crew are playing Shiritori after facing boredom in space. Then, they intercept Tsubaki's ship and accept Tsubaki's request, to get Tsubaki back to his own planet. Then, Bossun's ship receives space pirate Sōjirō's transmission. The space pirate demands Tsubaki's treasure while threatening to hurt Tsubaki's fiancée, Mimori.
Shinzou asks the Sket-dan for help with a makeover to make a good impression when he meets Megumi-dono, a friend he made online, in person. But is shinzou in modern clothes even him anymore? Can Shinzou somehow rectify his samurai beliefs with modern garb? Later, Himeko tries a new workout video, but it doesn't "work out"....
The Sket-dan get a new assistant homeroom teacher (who wants everyone to call her, Onee-san), but she's a klutz and is upset she can't be a good role model for the students, so the Sket-dan ask Chuu-san to help with some of his strange drugs. Later, Switch goes through some old inventions of his that didn't work out as intended...
In the second Arc finale, Switch's "origin story" continues as Sawa-chan goes to young Switch and his older brother for help from a stalker. In a moment of spite stemming from jealousy, though, Kazuyoshi sends Switch and Sawa off on their own to buy personal protection items. While they're gone, Sawa's friend Yukino warns Kazuyoshi that the stalker is also a slasher. Kazuyoshi means to go out after his little brother and the girl he loves, but fate intervenes...
The principal adores his grandson very much and asks the Sket-dan to prepare a picture play to entertain him. They decide to base the story off of Momotaro, but change things up from the usual... Afterwards, he asks them to play with his grandson for an afternoon, but the kid doesn't seem interested in having fun at all.
Bossun bumps into Himeko outside on the weekend, and they happen to spot Switch and Yuuki meeting up nearby as well. Their curiosity piqued, they decide to trail the 'odd couple' into a shopping mall. Turns out Switch is helping Yuuki with a request- to choose and purchase a laptop, so she can create a website dedicated to her passion of all things occult. Hijinks ensue, with the embodiment of 'Otaku' and 'Occult' clashing their interests and respective positions(supernatural vs science) against each other all the way(in their usual fashion). Nonetheless, they seem to be getting along well(again, in their own way), and even Bossun and Himeko note how unusual it is for Switch to be going out of his way to help his 'archrival', Yuuki. Switch and Yuuki then bump into her old crush from middle school, Kobayashi, who was there with another girl. He talks down to Yuuki, which seems to rub Switch the wrong way.
A writer for a local newspaper is coming to interview and take a photo of the Sket-dan, and Himeko demands that Bossun get his hair cut. But when Bossun refuses, Himeko takes things into her own hands... What could possibly go wrong? Afterwards, it's the principal's birthday, and the Student Council is planning a surprise party for him. But when the President makes a mess of his prized bronze bust, the principal will be in for a whole different kind of surprise...
Yamanobe-sensei is back, and now he's trying to get everyone in the Sket-dan to play a nutty board game called Hyperion. Everyone except for Himeko, as only men can appreciate this game, supposedly. But the epicness gets Bossun and Switch very enthused about the game, and soon they find themselves heading to the world tournament...
Bossun may have a way with words, but these clients were born with their feet in their mouths! First is J-son-sensei, the shop teacher with the glass heart and looks straight out of some horror movie! Can the Sket-dan help him find love? A man of few words and many offstandish poses, "Dante" perhaps poses the greatest riddle of all... Can the Sket-dan help this Fallen Angel find his Wings
Uchida Takaaki comes to the Sket Dance with a simple request: make him popular! Bossun and company immediately set their sights on getting Uchida to win a Mr. Popularity contest in their class, but Uchida's shy personality makes it difficult for him to stand out. Can Sket-dan Productions mold him into a star in just one week?!
The Sket-dan is having fun trying to take their minds off the upcoming midterms, when they hear rumors of a mysterious DVD that will curse you with bad luck if you watch it. Just then, Kuramoto Ayumi comes in with a simple request, to help cheer up her friend who has been acting strange lately. But there's more to this than meets the eye, as the stoic Yagi is acting like someone who has seen something they shouldn't have...
Yuuki Reiko, member of the Occult Club, barges into the Sket-dan's room holding a picture of one of Kaimei Academy's seven mysteries, the "Ghost of the Incinerator". The Sket-dan are on the case (mainly Switch), trying to find out the truth behind the picture, and getting Shimada Takako from the Newspaper Club mixed up in it, too...
A transfer student arrives on campus, and the three members of the SKET-dan introduce themselves, hoping the new student will join, but he politely declines. He returns soon after, covered in red paint as the apparent victim of bullying, asking the group for help. After investigating, they discover the culprit is actually the transfer student himself, who was operating under duress from the school bully and childhood acquaintance. After setting things straight, the new student is able to fit in comfortably at the school, and the members of SKET-dan look forward to their next task.