At the bottom floor of the building with a dog signboard, in the shopping district near the office street, there lies a cafeteria called "Youshoku no Nekoya," that has an illustration of a cat on the door. It's been open for fifty years and has satisfied various salarymen from nearby offices. Despite it being called a Western cuisine cafeteria, it also provides other varieties of menus. For the people of this certain world, it's their one-and-only special cafeteria. There is, however, one secret to "Nekoya." The cafeteria is closed to the public every Saturday in order to make way for special guests. When a bell rings, customers from different places of birth and races appear who ask for mysterious and delicious dishes. They are actually the same dishes served to the salarymen, but these special guests find them to be more exotic than to what they are used to. As the cafeteria aims to serve masterpieces, it is usually referred as "Isekai Shokudou." And so, the bell rings again this week.

Nearly half the population of Sakurada, a small town near the Pacific Ocean, has some sort of unique power. These powers range from being able to enter the mind of a cat, to resetting the world back to a certain point in time in the past. There is a group known as the "Kanrikyoku" that controls and monitors the use of these powers. Asai Kei and Haruki Misora work for their school's club called "Houshi" club, which execute any missions received from the Kanrikyoku. Misora has the ability to reset the world 3 days. This means that all events and any memory of the past 3 days that "could have" happened, never happened. Kei has the ability to "remember" the past. Even after Misora uses her powers to reset the world back 3 days, Kei will retain those 3 days in his memory. Combining their powers, these two solve missions issued by the Kanrikyoku.

Layton receives a letter from the famed opera singer, Jenis Quatlane, inviting them to see her newest performance. She also asks Layton, Luke and Remi for assistance in a mystery, saying her friend Melina died one year ago, but returned later as a seven year old girl saying she had found the secret of eternal life, and she also knew all the secrets that only the true Melina could know. Naturally, the case fascinates Layton and his apprentice, so they head to the Crown Petone opera house, but Remi stays in London, searching for some girls that went missing in there. The opera was about a lost kingdom, The Kingdom of Immortals; once, there was a beautiful queen that loved music. She was beloved by everyone in the kingdom. But one day, the queen became very ill. The people of the kingdom toiled to find a cure, but medicine couldn’t help. The queen finally passed away, and right after, the cure was completed: A potion for immortality. The people of the kingdom deeply lamented for the death of their queen. In order to the meet reincarnated queen again, they decided to become immortal, using the just-completed immortality nostrum. Abrosia's Kingdom is still somewhere in this world, waiting for its queen to return, and then, she will sing forever. After the spectacle finishes, a masked men appears, and proposes something to the audience: "Let's play a game"- he says- "The winner, will have eternal life. The losers, will have to die." It's up to Layton and Luke to enter in the game, and discover the secret of Eternal Life. (Source: Wikipedia)

In the year 2012 Japan was invaded by the Mu. Human-like beings from another dimension with blue blood. In the year 2015 Tokyo is attacked by invaders, who are repelled by a humanoid weapon called a Dolem. During the chaos, Ayato Kamina meets Reika Mishima, a classmate. During that same day, he is attacked by government officials but a woman named Haruka comes to his rescue, informing him that she was sent to get him by the Organization TERRA, and that Tokyo had been sealed in a time rift where time flows one third as fast as the outside world. He flees from Haruka onto a train where he sees Reika once more. Arriving at the Room of Rah, he follows her to a tremendous egg where the Dolem RahXephon is hatched from, and upon her singing his mother appears atop the Dolem that had stopped the TERRA Invasion. In the battle Ayato's mother is injured, and Ayato flees Tokyo Jupiter with Haruka.