Professor Layton's daughter, Katrielle Layton, runs the Layton Detective Agency together with the talking dog Sherl and her assistant Ernest, and solves strange cases that happen everyday in London. Originally, she started the job with the purpose of finding her father, Hershel Layton, who had disappeared suddenly, but her incredible ability to solve puzzles made her well-known and she receives numerous requests.

The story of the mecha anime revolves around 13-year-old Meguru Tokio, who is suddenly approached by a strange woman who is running away from something. She finds out that the girl's name is also Meguru, and although she appears to be around 17 or 18 years old, she has a passionate personality, which the younger Meguru has trouble dealing with. Meguru Tokio gets drawn into the older Meguru's fight with a mysterious organization, and gets targeted by the organization as well. The one targeting them from the organization was the narcissist, Rei. Although the younger Meguru can't believe that the older one came from the future, she fights alongside her in a dimensional robot. After fighting with Rei, she finds out that even though the other Meguru is older than her, she is Meguru Tokio's descendant. After finding out that someone has jumped into the past by the older Meguru's history surveillance device, the two also make a leap back into the past.

Not long after forming their partnership, detectives Ron Kamonohashi and Totomaru Isshiki have proven adept at solving various cases together. However, the two are further motivated to continue their work when they discover that the House of M—an infamous crime syndicate—orchestrated Ron's expulsion from the prestigious Detective Training Academy BLUE five years prior. It appears that this group is also linked to Ron's mysterious ability that causes those around him to lose their lives, a phenomenon which Ron is desperate to stop. A member of the House of M soon starts to commit boastful serial murders around Shibuya as an act of provocation toward Ron. Consequently, the investigative pair must do their best to apprehend the culprit for the sake of justice as well as learning more about Ron's dark past and present condition.

Fam and Ihrie are willing to do almost anything to make a buck. So when these debt-driven damsels discover the potential profits to be hand in recovering a particularly dangerous mystical object, it means mortal peril for an entire civilization. There's no guarantee that they'll live long enough to squander the fabulous wealth they've been promised, and danger lurks around every turn as they cross dark seas in pursuit of legendary evil. Haunted by an unspeakable curse, plagued by doomsday prophecies, plotted against by untrustworthy traveling companions and looked in desperate race to gain the Ultimate Power, Fam and Ihrie are the Ruin Explorers!