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.

Hayate asks Maria what she would like to get an idea of what girls his age want so that he can figure out what to buy Hinagiku for her birthday. Hayate goes into town and chances upon Ayumu, though they are initially awkward toward each other after remembering the events of Valentine's Day. Izumi, Miki, and Risa show up as well, and they help Hayate look for a present. Hinagiku finds them and finds out about Hayate looking for a present for her. Hayate says he does not have the financial means to support a girlfriend at this time, so while he does not dislike Ayumu, he cannot bring himself to get involved in a relationship.

Hina becomes preoccupied with why she has been thinking about Hayate so much lately. She finds out that Hayate is on the verge of failing to progress into the next grade, causing her to get very angry at him. Hayate goes to apologize, but he does not know what to say. When Sakuya breaks a cursed doll of Isumi's, a cross-dressing curse befalls Hayate, causing him to wear a maid uniform against his will, and if he does not beat Hina in a match before 9 PM tonight, he will have the desire to cross-dress for the rest of his life. Isumi gives a note to Hina to explain what she should do, but Hina takes this as a note of challenge, and does not intend to lose.

After Isumi's butler, Kotetsu, realizes Hayate is a boy, he becomes enraged, and tries to hunt down Hayate. Later, Nagi gives Hinagiku the watch she prepared for her birthday, and then becomes kidnapped by Kotetsu, who says to have Hayate rescue her. Meanwhile, everyone surprises Hinagiku with a surprise birthday party, and after being asked where Hayate's present is, Hinagiku misunderstands the letter of challenge as a way for them to be alone. After hearing that Nagi has been kidnapped, Hayate runs through the festival even though he is wearing embarrassing clothes. Nagi talks with Kotetsu about how shallow his love is, and how he only looks at the appearance of others. This opens Kotetsu's eyes and he confesses his love again to Hayate, but is beaten away by Nagi. Nagi also scares away the curse of the Hina Doll and Hayate returns back to normal. Finally, Nagi and Hayate head home, but Hayate remembers that he forgot to meet up with Hinagiku, and heads to the clock tower where Hinagiku is sleeping.

Hinagiku wakes to see Hayate, and after noticing the time, becomes enraged at Hayate's tardiness. She begins to attack Hayate with the Masamune Bokken she received from Isumi, and after a while, Hinagiku loses control of her emotions due to the sword and cries in Hayate's chest. Later, Hinagiku becomes embarrassed due to losing control of her emotions, and when she asks Hayate for her present, Hayate gives her some cookies he baked. Hinagiku then proceeds with telling Hayate about how her family also left her and her sister behind with a debt of 80 million yen and how she can relate to Hayate. Hayate leads Hinagiku to the terrace and makes her look at the view to make her feel better. After seeing the beautiful sight of the city at night, Hinagiku finally realizes that she is in love with Hayate.

Nagi wakes up after her dream where she became the number three spot in the Hayate the Combat Butler character rankings and Hinagiku became the top spot. On that night, Sakuya and Isumi are battling an evil eye yōkai, however they fail to catch its remainder. The next day, Maria gives bag to Hayate to deliver to Isumi because she is not feeling well. Hayate meets Isumi's mother and grandmother at the Saginomiya mansion. Afterwards, Isumi is attacked by the giant evil eye yōkai and Hayate saves Isumi. After leaving the Saginomiya mansion, a small person wearing a mask in all while attacks Hayate. Their battle ends abruptly to reveal the person as Ginka Saginomiya, Isumi's great-grandmother. She reverts to her old self again, and sucks Hayate's blood to gain back her youth. Hayate goes back home to the mansion, dry of blood and horribly thin.

Nagi decides to take Hayate and Maria on a trip to visit a mysterious meteorite that seems to enhance growth, along with other special powers. On the way there, Nagi accidentally leaves the train to buy a box lunch, but then the train leaves without her and she becomes lost all alone. Nagi meets up with Ayumu after eating at a ramen shop and Ayumu lets her ride on the back of her bike to take her to the next train stop. Meanwhile, Hinagiku tries to talk to Maria for advice about love, but they are interrupted by a call from Nagi. While waiting on hold, Nagi and Ayumu meet some hit men who say they need to take out Nagi but do not know which one is her due to both of them having pigtails. Ayumu pedals away on her bike, and Hayate is on the same road, looking for them.

Ayumu and Nagi manage to get away, but Nagi jumps off the bike soon after, telling Ayumu that she will be fine since Hayate is coming. Hayate finds Ayumu's cellphone and is promptly attacked by Ginka, Isumi's great-grandmother, who wants to take him to the Shimoda onsen. Ayumu comes back to Nagi to share a soft drink when the hit men return, and Ayumu and Nagi jump on the bike again to escape. Hayate and Ginka arrive, and Ginka takes care of the hit men, allowing the others to meet up at the train station in Asami. Nagi tells Hayate to bike Ayumu the rest of the way, and Hinagiku looks after Nagi and Maria on the train. Once in Shimoda, Nagi meets with Sakuya and the two go to a secret hot spring which causes Nagi to act like she is intoxicated, though it does not adversely affect Sakuya or Hayate who comes to retrieve Nagi. Later, an alien comes crashing into Nagi's room at night.

When Nagi wishes an alien on her mother's star,Nagi's wish become real Nagi helps the alien to find the spaceship. Hinagiku is relaxing on a onsen she decides to find and tell Ayumu Nishizawa the truth about that Hinagiku is fallen in love with Hayate. Then suddenly she passed out. Nagi and the alien found the spaceship and finds Hayate going to Isumi then Nagi and the alien follows Hayate. Hayate agreed to Isumi's great-grandmother he will give blood to Isumi to regain her powers but Isumi rejects the help of Hayate the great-grandmother of Isumi hits him with a morning star which cause him to bleed. Soon after Nagi and Hayate had a fight suddenly Nagi accidentally gets on the spaceship that she will never come back.

Ayumu realizes that despite telling him otherwise, she actually does want a White Day present from Hayate. Hayate buys a basket of cookies for Ayumu at Hinagiku's suggestion, but, nervous about presenting the gift to Ayumu, practices a greeting for Ayumu only to accidentally give the cookies to Maria instead. When Hinagiku discovers that Hayate neither gave the gift to Ayumu nor has enough money to buy another one, she brings Hayate to a friend's cafe in order to bake cookies. Despite Hayate's terrible luck, he manages to meet Ayumu and give her his White Day gift. That night, Hayate catches up to Hinagiku and gives her a present as well.

Nagi, having woken up after noon for all of spring break, resolves to rid herself of her hikikomori lifestyle. After Hayate accidentally breaks his cell phone, Hayate and Nagi go shopping in Shinjuku to replace it. Nagi gets lost, although she vehemently denies it, and is directed to the lost child section of the electronics store. Nagi challenges the boys there to a duel with the Hayate the Combat Butler Trading Card Game; she wins and tells the boys to call her "boss", after which Hayate arrives to pick her up. On March 29, Sakuya reminds Hayate that her birthday is on April 3. Knowing that Hayate cannot afford to buy her a present, she asks for a good laugh. In an attempt to learn how to be funny, Hayate forces himself to try and jab at Maria but instead trips and face-plants her chest. Nagi beats up Hayate as a result, and Sakuya gets the laugh that she asked for, although she tells Hayate that she still expects something on her actual birthday.

Father Linn Regioster suddenly appears before Hayate and announces his decision to rest in peace. However, he claims that to finally leave the Earth, he must rid himself of his one lingering regret by flirting with a maid. Since Maria cannot see Linn and because Hayate has no intention of letting Linn take over his body, Isumi resolves to learn how to be like a maid herself. After Nagi coaxes some advice out of Wataru under dubious circumstances, Sakuya introduces her maid Haru to teach Isumi the spirit of a maid. Much to both Hayate and Isumi's chagrin, however, the entire setup was an April Fools' Day joke by Linn.

Nagi tells Hayate how she came to adopt Tama during a trip in Africa. Tama, determined to get rid of Hayate and Shiranui, corners the latter in a delivery truck only to be locked in and transported to an unknown location. Fearing for his life after hearing that an anaconda loose in the city was shot and killed, Tama tries to make his way home with Shiranui. The two are saved by Hayate when he pulls them out of the way of a speeding truck.

Nagi asks Maria about the importance of money by which she understands how hard Hayate works to pay his debt off. She decides to give Hayate a birthday present,a wrist-watch which Hayate wants to wear all the time,by working for the money at a part time job. At the same time Hayate receives a call from an old cafe place he used to work for and finds out that he is needed there. Maria seeks this chance and replies on the phone that Hayate and another girl by the name Nagi Sanzennin will be working there. In the end it turns out to be a contest between Ayumu Nishizawa and Nag

Tired after a day's work, Nagi decides to take a nap even though Sakuya's birthday party is that same evening. At the party, Aika discovers that Chiharu works as Sakuya's maid. Meanwhile, Sakuya forces an extremely reluctant Wataru to entertain her and her guests; after Hayate and Nagi arrive, Sakuya manages to get Hayate to perform as well. Sakuya introduces her father and younger twin siblings to Hayate. After seeing Sakuya play with her siblings and her father, Nagi leaves. At Café Donguri, Hinagiku asks Ayumu to see the cherry blossoms with her, saying that she needs to talk with Ayumu about something important.

Ayumu takes Hinagiku to a Ferris wheel which overlooks a grove of cherry blossoms. At the Aizawa mansion, Nagi goes missing and Hayate and the others try to figure out where she is. Hinagiku tells Ayumu that she betrayed her and that she too is in love with Hayate, though Ayumu does not think that this is a big deal. Hayate finds Nagi on a balcony and wants to comfort her, but ends up destroying the atmosphere. Nagi tells Hayate that she will keep him close to her for the time being.

Nagi is forced to rest after coming down with a fever after a day of hard work. Nagi asks Hayate to do something that makes her sleepy, upon which Hayate tells a strange and nonsensical version of Alice in Wonderland. Bored, unable and unwilling to fall asleep, Nagi asks Hayate to get her some Packy and attaches a hidden camera to his tie for entertainment. Nagi and Maria watch as Hayate's terrible luck forces him to undergo a string of unfortunate events. Hayate ultimately makes some Packy himself and brings back one stick after narrowly being run over by a truck. A new semester starts at Hakuō Academy though Nagi is still unwilling to attend.