It's culture festival time and Hayate is kept busy by the students and teachers. Nagi searches for him, but she is unable to find him. A mysterious dark butler tricks Nagi and hypnotizes her. In her hypnotic state, she finds Hayate and leads him to the mysterious dark butler.

Nagi, still in her hypnotic state, helps organize the second day of the school festival with the help of Superintendent Kirika. They organize their own Comiket where Nagi sells her own dōjinshi. Kirika challenges Hinagiku to see if Nagi's dōjinshi or Hayate's butler cafe can make the most money. When Nagi tastes the cake that Hayate made for the competition, her hypnotic state goes away.

Nagi is having trouble writing a new manga, so she orders Hayate to go out and gather references for her. She also gives Maria and Klaus the day off because she feels she needs to be alone to concentrate. Maria tags along with Hayate and the two soon become uncomfortable because their joint effort to gather references feels like a date. Yukiji, Risa, Miki, and Izumi spot them and try to get the two to kiss by bringing them to the trendiest date spots. At the end of the day, Nagi shows Hayate her fiery wrath when he shows her the photo references he took, which are mostly pictures of him and Maria having fun together.

Klaus is feeling depressed after Nagi gives him permission to retire after he tells her about a dream he had, where he retired on a coffee plantation in Brazil. After Maria tries to convince Klaus to stay, Klaus decides to challenge Hayate to see who is the better butler. Klaus fails at this and has his mind set on retiring. Maria comes up with a plan that involves Hayate's female alter ego, Hermione. This plan fails as well and just before Klaus is about to leave, Nagi thinks of a way to make Klaus stay. Her plan succeeds and Klaus decides to stay as a Sanzen'in butler.

Nagi, Hayate, and Maria go to a Christmas party hosted by Nagi's grandfather. Just like the previous Christmas party, Nagi escapes - this time with Hayate. They head to the park where Nagi tries to make romantic advances on Hayate, but they are interrupted by a mysterious dark butler, Cyborg Butler, and Superintendent Kirika. Hayate is defeated, but they are saved by Himegami, who now calls himself Princess God. The next day, Hayate fails at all his butler chores and Himegami explains it is because Superintendent Kirika drained all his butler powers. In order to keep Nagi safe, Hayate resigns as Nagi's butler and leaves the mansion.

Kirika asks Hayate to wear the ancient butler robe which has been rejecting countless butlers. In exchange, she promises to leave Nagi and her fortune alone. Nagi, Hinagiku, and Himegami come to Hayate's rescue, but they arrive too late, as Hayate has turned into a nekomimi maid. They battle Kirika and Shion and during the battle, Nagi's pleas reach Hayate. The nekomimi maid uniform transforms into the legendary butler uniform. With his newfound power, Hayate defeats Kirika's snake, Jörmungandr.

On the night before New Years, Nagi orders Hayate to bring her to Kujukuri Beach to have a romantic date watching the sunrise after reading about it in a manga. Hayate is forced to take her on a bike since he is not old enough to drive. He manages to make it on time, but Nagi falls asleep just before the sunrise. The next day, the mansion's circuit breaker overloads and Hayate goes to the annex to turn it back on. On the way there, he gets stuck in a blizzard which is really caused by Sakuya's snowblower. He manages to turn the power back on, but passes out due to the extreme cold. After insulting Sakuya without meaning to, she (and her bodyguards) ditch him and leave him on a stretcher in the annex.

On the way the school, Hayate and Nagi bump into Hinagiku who is worried about her sister after she gave her New Year's allowance. Yukiji appears, shocking the three with an unusually cheerful attitude, giving Hinagiku a New Year's allowance because of a promise Yukiji made with her 10 year ago (although it was only 500 yen), and shocking them even more after they found a letter of resignation which dropped from Yukiji's bag. When homeroom ends, the class begs Yukiji to stay as a teacher causing Shiori to burst out in tears, who is happy that the class cares for her and decides to not resign. The resignation letter belonged to Shiori who found being Yukiji's superior harder than she thought. Yukiji was happy because she found many signs of good fortune.

Nagi, perplexed by Hayate's apparent lack of weaknesses despite being a main character, plots ways to find chinks in his armor. As her various schemes fail to produce results, Maria, Sakuya, and Isumi get swept up in the flow and discuss their weaknesses as well. Hayate and Wataru begin studying German in preparation for a Hakuō mathematics exam, while Maria tells Hayate a bit of background information on Isumi, Sakuya, and Wataru. When they go to check on Nagi and Wataru, Nagi becomes jealous that they are alone together, prompting Maria to remark that Hayate's weakness seems to be not understanding the female heart.

While working on her manga, Nagi gets the idea that, instead of chasing after Hayate to further their relationship, she must give him the cold shoulder and force him to chase her. A convenient invitation from Sakuya to a cruise on a familiar-looking ship gives her the perfect opportunity to set this plan into motion. As Hayate wanders around amazed, she shuns him over and over, culminating in the command to "explore the ship yourself". The ship is then threatened by a trio of terrorists, who are handily defeated by the Sanzen'in and Aizawa butlers; however, one of them sets off a bomb, blowing a hole in a cargo hold Hayate had just wandered into. There, he meets Isumi, who had become lost, in danger from a pair of large sharks. As the ship-goers are evacuating, Nagi remarks that Hayate hasn't shown up yet, and goes to search for him. She finds him holding off a shark; as she dives into the water to help, she is attacked by the other shark. Hayate defeats the sharks to save Nagi, but falls unconscious from the combination of the cold water and wounds he received from the earlier explosion. He is saved by Klaus, but Klaus' attitude causes Nagi to worry, as it has the effect she was trying to achieve herself.

Nagi completed an improved version of her manga, but still, no one can understand it except for Isumi. She takes Hayate, Maria, Isumi, and Sakuya out for ramen, but they find themselves in a hidden animation studio where they are shocked to hear that Nagi's manga is going to be animated. The directors declare Nagi's demands to be impossible, but they end up animating it anyways because of a rumor that their stock will go up if they do it. After the premiere one week later, everyone is at a loss for words.

Nagi surprises Maria with an overnight relaxation tour at the Hyatt Regency hotel after Maria becomes upset when Nagi and Hayate thought she looks older than her actual age. When Hayate orders for room service, they meet Izumi to find out the students of Hakuō Academy are running the hotel for a one day experience event. Maria enjoys a few of the hotel facilities until the students are unable to accomplish their jobs and ask Maria for help especially when the Kirika and Shion visits. Maria spends the rest of the day helping the students in secret from Nagi and Hayate.

Wataru is shocked one day when he sees that Isumi is wearing a different school's uniform and can even get from one point to another without getting lost. Wataru seeks help from Nagi, and eventually going to the high school he saw Isumi go to earlier. Wataru finds Isumi showing a lot of attention towards the pitcher on the baseball team, which leaves him to jump to conclusions. It turns out Isumi was merely trying to exorcise the spirit of a girl who had liked the pitcher. Wataru challenges the pitcher to a match for Isumi's heart, but loses which greatly depresses him. Isumi succeeds in exorcising the spirit, and thanks Wataru for his help, which relieves Wataru of his worries about Isumi.

Due to Hayate's most recent borderline test scores, Nagi gives him some time off to study. Meanwhile, Klaus sends a robotic butler which looks somewhat like Hayate to fill in for him while he is studying. The robot, known as Thirteen, does an even better job as a butler than Hayate even could, which depresses him when he finds out. Thirteen devises a plan to get Hayate and Nagi alone together, though only Hayate realizes this after the fact. That night, Thirteen goes into space to destroy a meteor heading for Earth, but is stranded on the moon with no power in the process of saving Earth.

Nagi is planning a celebration party for Hayate for graduating, though gets him to stay out of the mansion for a while by giving him the task of retrieving a small box carrying an item she bought off the Internet. While out, Hayate is offered 150,000,000 yen by a national escort service in order to recruit him into their business and so that he can pay off his debt to Nagi. While thinking this offer over, he loses the box and has to go halfway around the world in order to retrieve it, though by the time he gets back to the mansion its already dark out. Hayate is very grateful to Nagi for the party, and the item he retrieved which was intended for him, and turned out to be a small pocket watch. Hayate later turns down the offer from the escort service, and it turns out that Nagi's grandfather set up the offer in order to test Hayate's loyalty.

During Golden Week, Hayate, Nagi, and Maria take a trip to an island in the Aegean Sea. Nagi still does not like to go outside much, though she gives in to Hayate after he sulks. While out the next day, Nagi's hat is blown away by the wind, and when Hayate goes to retrieve it, he falls into a time slip and arrives many years previous when Nagi was living on the island. After he realizes what is going on, he discovers she is being targeted by the Mafia, and he ends up protecting her from them, ultimately winning; Hayate realizes that the reason he was sent back was to save Nagi. Hayate had promised Nagi in the past to watch the stars together at the beach, but when they go at sunset, Nagi's hat once again is blown away and Hayate goes through another time slip back to the present. This caused Nagi to remember Hayate in the past as a liar who disappeared on her and took her hat with him. Back in the present, Hayate gives Nagi back her hat and the two gaze at the starry night sky together.

A marathon is coming up at Nagi's school, and Maria and Hayate want her to participate too. Nagi makes a bet with Klaus, where if she can get in first place in one of the races, then that would prove Hayate's worth as a butler, but if she cannot, then Hayate will be fired. Hayate trains with Nagi the next two days, and the day of the race the two get off on a slow start. Before long, Hayate must carry Nagi throughout most of the race, and faces a few enemies along the way impeding their progress. After running into Hinagiku, Nagi goes on ahead, but just as she is about to win, Hinagiku's older sister Yukiji beats her to the goal, winning the 150 million yen prize.

As stipulated, Hayate is to be fired as Nagi's butler, but as Klaus fears getting fired himself for this, he sends Hayate off to be trained at the Tiger's Den for Butlers to show his worth. Hayate meets a Catholic sister on the train, Sister Fortesia, and he later meets her again at a church which doubles as the location of the Tiger's Den. The next day, Hayate must find three others to go on a Butler Quest in an underground dungeon as a part of his training. Nagi is quick to join, and Yukiji and Wataru also join in.

Hayate and his party members continue to go on the butler quest. Hayate is poisoned by a poisonous spear after saving Nagi's life. Meanwhile, Hinagiku and Isumi are on the quest to help Hayate and exorcise this evil spirits, respectively. Hayate's group encounters the now-dead, ghost priest of the church, Rin Regioster, who points out Sister Fortesia to be a fake. The sister is takes control of a plug-in giant size robot to enact her revenge against the Sanzen'in family. While Fortesia and Hinagiku are fighting, Yukiji is possessed by an evil spirit, and attacks the others, also using the giant robot. Hayate exudes more power and destroy the robot, while Isumi exorcises the spirit possessing Yukiji. Back at the mansion, Hayate collapses after the butler quest.

One day before valentines, Nagi is trying to make some chocolate for Hayate and decides to skip school. At school Nishizawa tries to give Hayate some "love chocolate" but insteads gives him obligation chocolate. Hinagiku realizes Nishizawa panicked and tells Hayate to exchange it. However after receiving the "love chocolate" Hayate is a bit confused on the love concept and asks Maria for help. Maria remembers that she had little/no experience with love either and becomes depressed/mad. However she decides to make some chocolate for Hayate. Nagi, after failing herself to make chocolate, tells Hayate to make some chocolate for her. Hayate meets Maria in the kitchen and they have a contest to make the best chocolate. Maria makes her chocolate super incredible, but when asked about who its for, she becomes embarrassed and runs outside. Hayate catches up to her and gives her some chocolate that he made, and says valentines is the time where people work harder just to see the person they treasure smile.

Maria explains how Nagi developed an inferiority complex due to her short height causing her to frown most of the time. Kazuki, Ayumu Nishizawa's younger brother, confesses to Nagi about his love for her and asks if he is able to take Nagi on a train ride, though it becomes a date. At the end, Kazuki says that they should do things like this again. Nagi says that it is impossible because she already likes someone, but Kazuki says he has not given up. Back at the mansion, Nagi becomes dejected because Hayate has not become jealous about her date with Kazuki. Later, Nagi takes a bath, with Maria helping her wash her hair. Maria leaves for a bath towel, but due to a sudden visitor, she asks Hayate to bring a towel to Nagi. Hayate walks into the bathroom and accidentally sees Nagi naked. Hayate asks if Nagi is mad at him, and she says she is, but she says she forgot why she was mad, and kisses Hayate on the cheek.

Nagi is feeling embarrassed after kissing Hayate on the cheek, and she sends him out the house. Maria gives Hayate one million yen to go live outside the mansion for three days, but he uses the money to help people in need. Broke and having nowhere to go, Hayate is in the park reflecting on his position, when Hinagiku invites him to her house. Hayate stays for the night, and Hinagiku comes into Hayate's room. Hayate becomes flustered when he sees Hinagiku and notices her beauty. Hinagiku as well becomes flustered when she wants to ask Hayate about his relationship with Ayumu. The people that Hayate helped come back to the mansion and give all the money back. Maria notices that Hayate gave away his living expenses and decides to find out where he is staying. Maria decides to infiltrate the school to do so, and meets Hayate on the elevator for the school clock tower, although he is clueless that she is really Maria.

Hayate and Maria get stuck inside the school's clock tower elevator where Hayate realizes Maria is disguising herself. Nagi calls Maria on her cellphone due to her clumsiness with making tea, and Maria goes back to the mansion. Hinagiku and Hayate go to the supermarket and talk with each other, and also make dinner for each other. Hinagiku asks Hayate if he has a girlfriend, but he says he does not. Hinagiku goes to a supermarket and meets Ayumu who is eating baked yams. Hinagiku talks to Ayumu about what happened during Valentine's Day, and if she has a relationship with Hayate. Hinagiku sees a little kitten, and decides to take it back home. Hina feeds the kitten milk, but Hayate says they cannot sleep because they need to take care of the kitten. Maria asks if Nagi wants Hayate to come back to the mansion the next day, and she says she does.

Hayate goes back to the mansion with the kitten, and Nagi instantly decides that she will raise it and names it Shiranui. Tama becomes jealous of Shiranui, and tried to make it seem like Shiranui ripped up Nagi's manga, but the plan backfires when Shiranui rips of the manga, and makes it seem like Tama did it. Nagi locks Tama in a cage for a little while as punishment. Isumi comes over to play with the kitten, but Shiranui becomes vicious towards her, and makes Isumi feel horrible. Isumi asks Sakuya for help, who suggests a change in attire, since she always wears traditional clothes. After changing into more casual clothing, Sakuya and Isumi head over to Nagi's mansion. Hayate helps Isumi by spraying diluted cat nip on her, causing Shiranui to become playful towards her. Nagi and Isumi play with Shiranui, and Nagi lets Tama play as well.

Sonia (the nun) is outside Wataru’s Video Store debating to herself about her love for Wataru, she finally says she just wants to acknowledge her feelings and goes in the store. She realizes that she is truly in love with Wataru but becomes jealous when Wataru takes care of Saki when she falls. The two kidnappers from the 1st episode try to kidnap Wataru, but they accidentally kidnap the Saki instead. Wataru gives Sonia a kiss on the cheek to save Saki and she does so easily. Sonia goes into the video store again, and Wataru lends her another video, but this seems to get Saki jealous. Later, Katsura sensei has been asked if she has a boyfriend, and she makes up a lie saying that she has dozens and chooses one to be with depending on her mood. To get a boyfriend Katsura sensei asks Nagi when the next high society party is, and Klaus says they will have one tonight. To prepare for the party, Katsura sensei goes around and asks people for advice about love. Miki, Izumi, and Risa go directly to Hayate for help on this matter. Nagi talks to Katsura sensei about having a boyfriend, and after a little bit of thinking Katsura sensei says she actually prefer booze instead. Everything goes well for Katsura sensei, but in the end, we see Maria sighing about having a boyfriend.