Kyouhei, after moving away to Tokyo from his old town to get away from the events that happened, is on a goukon with his friends, including his old neighbor, Shiba. After drinking for a whole night, he and Shiba discover a dead, bloody body in the elevator. He is told by his younger sister, Utao with her Kamisama Doll, that Aki, an old friend, and his Doll are the culprits responsible.

Taking place one month after the events that occurred in the movie Heaven is a Place on Earth. Living at the Sanzenin Mansion once again, Nagi returns to her old ways of life, until she receives word from American authorities informing her that she has a week to pick up her late father's belongings that was indefinitely delayed due to various circumstances. After receiving news of her father whom she doesn't remember, Nagi then meets a mysterious girl (with a hidden agenda) claiming to be Nagi's little sister. The series tells a new story that is original to the anime and not directly based on the manga. The main author of the original series Kenjiro Hata personally created the original concept for the story of this anime. (Source: Hayate no Gotoku! Wikia)

After Junpei botched the second attempt to transport back to Japan, the four embark their journey once again to collect runes imprinted on skin of Elven females by stripping them. Celsia is cursed into the form of another animal this time. (Source: ANN)

In Martian colony Fourth Tokyo lies a classroom of Kirishina Corporation's brightest minds spearheading aerospace development: A-TEC, led by genius engineer Kaito Sera, eagerly anticipating the arrival of their newest member. It soon becomes clear, however, that the transfer student is hardly ordinary—Nagisa Kiryuu, newly appointed chief of A-TEC and the younger brother of the corporation's CEO, is sent to shut the program down. To keep the classroom alive, Kaito and his students desperately work to develop a successor to their most powerful rocket, the X-2; meanwhile, Nagisa climbs the corporate ladder in pursuit of his own mission. In spite of this, their separate battles soon reveal that much more is going on in Kirishina Corporation than meets the eye. Classroom☆Crisis follows Kaito and Nagisa, as well as Kaito's younger sister Mizuki and A-TEC's test pilot Iris Shirasaki, in a story of intrigue, political warfare, and, against all odds, romance. As Nagisa and A-TEC are dragged further and further into Kirishina Corporation's conspiracies, friendships grow and pasts are unveiled as they fight to avert their classroom crisis. [Written by MAL Rewrite]