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?

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.

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!

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.

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?

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?

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.

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.

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.

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.

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.