As the SOS Brigade shoot more of their film, Haruhi tries to give Mikuru another contact, ergo another superpower. Yuki quickly takes action and injects her with more nanomachines before any damage could be done. Despite the weird phenomena Haruhi's film is causing, Itsuki suggests it is better than more closed spaces being opened up. However, when Kyon discovers Haruhi arranged for Mikuru to be drugged for a kiss scene with Itsuki, he gets furious at her shabby treatment of Mikuru and almost hits her, forcing Itsuki to hold him back. This causes Haruhi to become depressed, having always thought Kyon would support her. Kyon, reluctantly learning something from Taniguchi, later apologizes to Haruhi and filming resumes. However, he seems to have inadvertently encouraged Haruhi even more, making cherry blossoms grow out of season.

One night, Haruhi's power is activated without her knowing, and both she and Kyon become trapped in a sealed reality at their school. As Haruhi goes out on her own, Kyon is met by Itsuki, who tell Kyon that Haruhi might have created this world to be alone with Kyon. Yuki contacts Kyon via computer and gives the hint of Sleeping Beauty as a means to return back. Kyon and Haruhi are forced to evacuate when blue giant entities appear and begin to destroy the school and the surrounding area. Using hints provided by Yuki and Mikuru beforehand in order to defuse the situation and escape, Kyon kisses Haruhi as he expresses his desire to return to the old world. It remains unknown whether or not this world is the old one or a new one, however the three other members are glad to see Kyon back again.

On the day of the school's cultural festival, the members of the SOS Brigade are involved in different activities. Mikuru and her class open a fried noodles café, Yuki attempts fortune telling, and Itsuki is in a play. Kyon attempts to enjoy a normal day. Kyon goes to the auditorium, where bands are playing for the audience, and falls asleep. When he awakens, he sees Haruhi walking on stage in a bunny girl costume with a guitar hanging from her shoulders.

Hoping to reclaim the computer Haruhi extorted from the Computer Research Society earlier in the year, the Computer Research Society president challenges the SOS Brigade to a computer game they created for the cultural festival entitled The Day of Sagittarius III. Haruhi accepts his challenge, but soon finds out that playing the game is much harder than she thought. Yuki is initially mystified by the computer's operation but catches on quickly, as she will tend to do. Eventually, she manages to find out that Computer Research Society club members are cheating and is able to block and use it against them, thus winning the game and some laptops for the SOS Brigade club room.

Kyon is dragged into helping Haruhi attempting to investigate what happened to Ryoko's strange disappearance without notice. After a fruitless search, Haruhi tells Kyon about her earlier years, and how she changed from an ordinary girl into her present state. Later that day, Itsuki tells Kyon about the theory of the anthropic principle correlating with Haruhi, and he believes that Kyon is the reason why Haruhi was able to wish of such extraterrestrial beings to exist. Itsuki brings Kyon into a sealed reality, where the latter watches the espers destroy a blue giant entity subconsciously created by Haruhi. When returning to his house, Kyon is told by Itsuki to look after Haruhi.

The SOS Brigade is going on a summer retreat. And what better way to enjoy a summer retreat than on a deserted island? But if the mysterious island mansion doesn’t live up to Haruhi’s expectation, will she cause another incident? Or something worse?

A new visitor appears with Mikuru to enlist the SOS Brigade to find her missing boyfriend, who happens to be the computer club president that Haruhi extorted. As they go on the hunt for him, a closed space begins to form. Can they save him in time?

Kyon is still processing what Yuki told him. Meanwhile, Haruhi’s wish comes true! A mysterious transfer student appears and joins the club. With five members, they can finally start on… whatever they do! But what’s up with the crazy reveals from everyone?

Things are back to normal. Well, as normal as life can be with Haruhi. So of course she wants them to enter… a baseball tournament?! But when the game doesn’t go the way Haruhi wants, danger lurks just around the corner. They’ll have to win, or else.

Haruhi gets her wish for a murder mystery when the master of the house is found dead! But an actual murder may be more than she can handle. As they work to solve the case, things become more and more dangerous. Can they figure it out?

The skies are overcast with a chance of rain, and Haruhi instructs Kyon to go pick up a heater. With Kyon gone, Haruhi takes pictures of Mikuru in various costumes for the movie's DVD cover, Itsuki helps how he can, and Yuki is left alone to read. After Kyon returns, he finds only Yuki in the club room and decides to wait for the others, but falls asleep. When he awakens, he finds Haruhi alone with him, waiting for him to wake up so they can leave. It has already started raining, so Haruhi borrows an umbrella from school for them to use. When returning home, Kyon finds a more playful side to Haruhi and in the end, she pulls a playful tongue-out face.

Haruhi is visibly bored and is not her usual energetic self. Ryoko Asakura, the class president, is concerned and asks Kyon to help her. Kyon later finds a mysterious letter in his locker, which directs to come to a classroom, where Ryoko confronts him. Revealed to also be an alien, Ryoko attempts to kill Kyon in order to provoke a reaction from Haruhi, but is stopped by Yuki. Later, Kyon meets Mikuru's older self that had traveled from the future, who reveals that Snow White is the clue essential to his future. Ryoko was reported to never have transferred into the high school, much to Haruhi's suspicion.

Haruhi Suzumiya is an eccentricity who dislikes the ordinary. If she could just meet an alien, time-traveler, or esper, her life would be made! Unfortunately, things just aren’t interesting. Until she decides to shake things up with her own club.

Deciding Yuki needs a familiar for her role, Haruhi picks up a stray cat and names it Shamisen. However, when Haruhi leaves that day, Shamisen starts talking as a result of Haruhi's powers. Itsuki suggests that they need to remind Haruhi her movie is a work of fiction, before reality takes any more damage. The next day at school, Mikuru gives him a coupon for her class's yakisoba café, and gives her views on Haruhi that she couldn't say in front of Itsuki. Kyon later talks with Yuki, who throws up the idea that one of them, including herself, may be lying. As shooting resumes, Haruhi's powers to continue to make Mikuru a deadly weapon. Itsuki calls Kyon out later that night, asking him to find a way to hold back Haruhi's powers. Kyon convinces Haruhi to add a disclaimer at the end, saying the film is a work of fiction, and the rest of the shooting goes without a hitch. Kyon falls asleep whilst editing the movie, only to find it has edited itself overnight. At the very last of this episode, there is a flashback to May that Kyon tries telling Haruhi that Yuki, Mikuru and Itsuki are actually aliens, time travelers and espers, but she doesn't believe him.

The SOS Brigade is now open! First, they need a computer for their club, and Haruhi is determined to get one. But is extortion the answer? Next, they need more members. And that requires… bunny outfits?! Finally, Yuki opens up to Kyon with a bizarre reveal!

All of their hard work is finally done. The SOS Brigade shows off their feature film! A tale of battle waitresses from the future fighting against evil, alien witches, and teenage espers. It will probably make sense… right?

The future Mikuru tells Kyon where to find a certain person that he is supposed to help. Kyon and Mikuru travels back in time to the Tanabata of three years ago. Carrying the sleeping Mikuru, Kyon finds the young Haruhi herself from middle school. After helping her draw strange drawings on her school yard, Haruhi questions him on the existence o aliens, time travelers, espers, or sliders; and Kyon suggests that they might. After Haruhi leaves, Kyon wakes up Mikuru and finds that she has somehow lost her time traveling device, or TPDD. He takes her to the Yuki of three years ago and helps them return to their proper time.

North High School is preparing for the North High Festival. Kyon and Haruhi's class, class 1-5, decides to do some questionnaire. Haruhi does not like that decision and tells Kyon that the SOS Brigade will do something more interesting. She decides to make a movie clip that has Mikuru as the protagonist. One day, after school, Haruhi, Kyon, and Mikuru go to stores in order to get a camera and airsoft guns.

Preparation for the SOS Brigade's short film continues, with character roles revealed—Yuki as an evil alien, Itsuki as an esper, and Mikuru as a battle waitress from the future. Mikuru is forced to dress in an embarrassing waitress costume for her role, while Yuki appears as a witch. On the first day of filming, the Brigade film two commercials to advertise their sponsors with Mikuru dressed in her waitress costume and then her bunny girl costume, much to her embarrassment. They then film several scenes in a park, and Kyon points out that Haruhi did not actually write a script.

Shooting of the SOS Brigade's short film continues. During the battle scene, Haruhi is displeased with Mikuru's acting. She yells at her, demanding that Asahina try to shoot a laser beam from her contact-lens-colored eye, but Kyon manages to cool her down . Afterwards the scene is reshot but, to the surprise of everyone except Haruhi, Mikuru actually shoots laser beams from her eye. Yuki knocks Mikuru down and apparently takes her contact lens. In a conversation Itsuki explains to a shocked Kyon that Haruhi changed reality once again and Nagato proves his words by showing her hand, burnt while protecting Kyon from being hit by the laser. Koizumi promises to take care of Mikuru's problem with Yuki's help. The rest of day is spent on shooting more scenes with Mikuru dressed as a bunny girl. The next day Kyon finds out that Haruhi dragged Tsuruya, Taniguchi and Kunikida to help. After Haruhi gets off to pick up Mikuru, Itsuki explains to Kyon that Yuki succesfully helped Mikuru get over herself. Haruhi returns with Mikuru, who secretely tells Kyon how Yuki helped her: she bit her to inject nanomachines into her body. Haruhi leads everyone to the next shooting location, a lake near Koizumi's house.

The previous time loop continues for the 15,513th time. This time, Kyon mentally senses an even greater familiarity with events and places from previous cycles. Once again, none of the Brigade members can devise anything to stop the cycle from repeating. On their final meeting in the restaurant, Kyon tries to call out after Haruhi but fails to do anything as visions of the loop's events flash in his mind. As Kyon regains his senses, Haruhi has left. As the last day of vacation arrives, Kyon, resigned to the loop repeating itself, goes to bed without finishing his summer homework.

After the busy island adventure with the SOS Brigade and a family trip to visit relatives in the countryside, Kyon is just settling in to relax for the final two weeks of summer vacation. Unfortunately for him, Haruhi wants to get everything she can out of the precious time remaining, in the company of the SOS Brigade. As such, the group is taken on a whirlwind tour of summer activities, from swimming pools to summer festivals, part-time jobs, and bug hunting. Finally, Haruhi has made it through her entire list, and the last day of August arrives. Though Kyon tries to make up for lost time by doing his neglected summer homework, he eventually gives in to distraction, going to bed just before midnight.

Like the previous episode, Kyon's easy going summer vacation is interrupted as the group is taken on a whirlwind tour of summer activities, from swimming pools to summer festivals, part-time jobs, and stargazing. However, Kyon is wracked by a constant sense of déjà vu. Koizumi is likewise troubled, while Nagato seems even more detached than usual. They finally work out the truth: Haruhi has put the last two weeks of August into an infinite loop because she refuses to let summer end. They find out that the loop has repeated 15498 times. However, none of them can devise anything to stop the cycle from repeating. On the second-to-last day of summer, Kyon calls out after Haruhi in a last-ditch attempt to stop her from leaving unsatisfied, but fails to think of anything he can do, and she leaves. As the last day of vacation arrives, Kyon, resigned to the loop repeating itself, goes to bed without finishing his summer homework.

The same exact events in the previous episode once again unfold with slight variations and the gang wearing different clothes. Once again the Brigade, with the exception of Haruhi, finds out that they are trapped in an infinite loop. In this 15,499th loop, Kyon and the others once again are unable to discover how to escape the endless summer. In the same scene in the restaurant, Kyon is unable to stop Haruhi from leaving, hence dooming the world to another summer loop. Kyon again goes to sleep without finishing his homework on the last day of summer.

The previous time loop continues for the 15,521st time. As the last day of vacation arrives, Kyon stays up late until midnight finishing his summer homework alone without any assistance. The final scene shows Kyon's clock ticking away on his desk but cuts out to the ending video one second before the clock strikes 12:00am.