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?

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.

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.