The sole thing that gets the middle-aged Sasaki through his soul-sucking job is a cheerful smile from Yamada—the young woman who works at a nearby 24-hour supermarket he frequents. After every tiring day of getting berated by his boss, Sasaki stops by the store to have his spirit healed by his favorite cashier.

After a particularly grueling day, Sasaki shows up at the supermarket, only to find that Yamada's shift has already ended. Disappointed, he searches for a place to smoke when a woman from behind the store calls him over to join her. The bold and dangerously playful Tayama is quick to call out Sasaki's peculiar habit of always seeking out her coworker—even going as far as telling Yamada about Sasaki's vested interest in her.

Now, in addition to seeing his adored cashier Yamada, Sasaki also visits the store to see if his new smoking partner Tayama is around. But there is more to Tayama's mischievousness than she initially lets on. With every cigarette, an unlikely friendship begins to blossom. 

Fifteen years ago, disaster struck human civilization, and now dangerous man-eating monsters roam the ravaged lands, posing an existential threat to the remaining survivors. Amid this turmoil, an isolated facility shelters children and nurtures them in peace. However, as a few among them find out about the world beyond the narrow periphery of their nursery's walls, their curiosity about it slowly grows.

Meanwhile, in the outside world, young survivors Maru and Kiruko band together to search for a special place called Heaven, each for their own reasons. Carrying past burdens and tragic secrets, the two hope to find answers to the cruelty they have experienced in their lives and in the world, which still remains in tatters.

If a survey were conducted to see if people believed in aliens, time travelers, or maybe espers, most would say they do not; average high school student Kyon considers himself among the non-believers. However, on his first day of school, he meets a girl who soon turns his world upside down.

During class introductions, the beautiful Haruhi Suzumiya boldly announces her boredom with "normal" people and her intention of meeting supernatural beings. Dumbfounded, Kyon learns of her frustration with the lack of paranormal-focused clubs at their school and unwittingly inspires her to start her own club. She creates the Spreading Fun all Over the World with Haruhi Suzumiya Brigade, otherwise known as the SOS Brigade.

Following the SOS Brigade's founding, Haruhi manages to recruit Kyon and three other members: quiet bookworm Yuki Nagato, shy upperclassman Mikuru Asahina, and perpetually positive Itsuki Koizumi. Despite their normal appearance, the new members of the SOS Brigade each carry their own secrets related to Haruhi. Caught up in the mystery surrounding the eccentric club leader, Kyon is whisked away on a series of misadventures by Haruhi and the SOS Brigade, each one bringing him closer to the truth about who and what she is.