Taking place in the alternate reality of the world Nagato created, everyone finds themselves in different situations. Yuki Nagato, who is not an alien but a cute, shy bookworm is desperate to keep the Literature Club alive. With the help of her best friend Ryoko Asukura, who is no longer a psychotic killer and Kyon, a very sarcastic guy who is still very sarcastic whether he's in the old world or the new one, do all they can to help Yuki.
Later on in the story, Yuki meets Mikuru Asahina, a cute moe blob and Tsurya-san who is Mikuru's best friend, along with Haruhi Suzumiya who is an eccentric girl with an interest in aliens, time travelers, and espers, and Itsuki Koizumi, a "mysterious" transfer student who attends the same school as Haruhi. The seven not only hang out together, but do all they can to help Yuki have hope and also help her blossom in personality.