The Melancholy of Haruhi Suzumiya Vol. 9 — Manga Raw / Buy Official

The culprit who altered the world was Yuki Nagato herself, acting against the will of the Data Integration Thought Entity to grant her own wish. After accumulating countless errors, Nagato began to feel emotions and, longing to "live as an ordinary girl," rewrote reality. Kyon chooses the original world, showing he's even prepared to shoot himself to launch the restoration program, then loses consciousness. He wakes to find everything restored—the SOS Brigade and Nagato are back. Kyon thanks Nagato, and finally admits, clearly, that what he truly wanted all along was the "extraordinary."