In the beginning, God created the heavens and the earth. He also sought after a wide variety of animals to populate the planet. However, he felt that it was too tiresome to think of new ideas within his criteria. To address this problem, God appointed an organization—the Heaven's Design Team—to do the work instead! Shimoda is a newly-hired angel who serves as the mediator between God and the design team. As he steps into his role, he witnesses his coworkers conceive interesting ideas for many unique life forms according to God's desires. From giraffes and snakes to birds, anteaters, and everything in between, the possibilities for different animal species are endless!

In a familiar yet different universe, shy bookworm and gamer Yuki Nagato is the president of North High School's Literary Club. Her friends, the overly-cautious Ryouko Asakura and completely average Kyon, are the only other members of the club. Nevertheless, Yuki enjoys the peace and quiet she shares with them, especially when she is with Kyon, whom she has a crush on. Added to the mix are Tsuruya and Mikuru Asahina, two friends with opposite personalities who frequently stop by the Literary Club. While walking back to her apartment on a cold December day, Yuki is coerced into drawing strange symbols on the ground by a girl supposedly attempting to capture Santa Claus. The girl introduces herself as Haruhi Suzumiya, an eccentric student from the prestigious Kouyouen Academy who is on the hunt for aliens, time travelers, and espers. When Haruhi and her friend Itsuki Koizumi make a sudden appearance in the clubroom, they declare themselves as official members of the Literary Club, with Haruhi taking up residence as the executive president. With the tranquil days of the Literary Club now behind them, Yuki and her friends get caught up in a series of misadventures under Haruhi's leadership—with each incident bringing Yuki and Kyon closer than ever before.

High school girl duo Popuko and Pipimi are back and more unhinged than ever after their initial efforts to create a full-fledged anime production were met with a great reception. With no regard for their audience, they continue to live their reckless everyday lives consisting of comedy skits and parodies of epic proportions. No one is immune to the effects of their antics—including hapless live actor Shouta Aoi, who is on the run and stuck trying to be a hero in the wrong series.

When Yun Arikawa and his partner, Haberu Katou, investigate a house rumored to be haunted, the last thing they expect is to stumble into a mystery that will soon envelop the entire planet. While measuring strange radio signals, they receive a call from Mei Kamino, a graduate student investigating the same signal and using the equipment their company previously installed. After an odd night, Yun returns to work at Ootaki Factory, a tech company that actually exists to produce Jet Jaguar—a robot that conspiracy theorist Gorou Ootaki has dreamed of creating. However, when flying dinosaur-like creatures known as Rodan are attracted to the strange radio signals, Jet Jaguar seems to be the only force capable of fighting them. As Yun and Mei investigate the Rodans' sudden appearance, more dangerous monsters begin to surface from the ocean—along with enigmatic red dust.