After being hit by a truck in the year 2014, Akira Natsume awakes to find himself inside a machine following a 16-year-long coma. As he adjusts to the new interface, he is greeted by police officer Minami Uezono and her android partner Alma. The pair shows Akira that his brain is contained inside a device called an EX-ARM—a weapon of mass destruction. Aboard an enemy smuggler ship, the three must escape using nothing but their ingenuity and combat skills. While initially reluctant to fight, Akira soon recalls his brother's words from before the accident. The memory inspires him to take action, possessing Alma's body to fight his opponents using martial arts. Once Alma plugs him into one of the ship's ports, he discovers the devastating potential of his EX-ARM by effortlessly hacking and assuming control of the vessel. Upon safely arriving back on land, Akira meets the other members of the EX-ARM Countermeasure Prevention Team, a police division working to mitigate the effects of EX-ARMs. Witnessing the atrocities committed by those who seek the power of EX-ARMs, he resolves to join the team and put an end to the terror caused by these weapons.

The start of Hanae Ashiya's high school career has not been easy—he has spent all of the first week in the infirmary, and his inexplicable condition is only getting worse. The cause of his torment is the mysterious fuzzy creature that has attached itself to him ever since he stumbled upon it the day before school began. As his health continues to decline and the creature grows in size, Hanae comes across a flyer advertising an exorcist who expels youkai. Desperate and with nothing left to lose, he calls the number and is led to the Mononokean, a tea room which suddenly appears next to the infirmary. A morose-sounding man, Haruitsuki Abeno, reluctantly helps Hanae but demands payment afterward. Much to Hanae's dismay, he cannot afford the fee and must become an employee at the Mononokean to work off his debt. And to make things worse, his new boss is actually one of his classmates. If Hanae ever hopes to settle his debt, he must work together with Abeno to guide a variety of dangerous, strange, and interesting youkai back to the Underworld.

Despite being burdened with crippling debt to the morose Haruitsuki Abeno, Hanae Ashiya has come to enjoy his job as an exorcist. His ability to communicate with youkai has given him a sense of responsibility regarding the magical creatures, and he continues to work hard to send them to their true home in the Underworld. As Ashiya’s life finally stabilizes, the youkai threaten to upset it once again. Knowledge of his existence has begun to spread, and not everyone is happy to have a human working for the Mononokean, the interdimensional tea room. But one day, a simple visit to the Underworld draws the attention of those in power, and Ashiya soon learns that not every youkai is willing to go along with Abeno's plans.

A new era of exploration begins with the sudden appearance of a new continent known as Magmell. Magmell's vast trove of never-before-seen natural resources spurs on the exploration of its vast landscape. However, the unknown is not always docile. In order to sustain the expeditions, people known as anglers specialize in dealing with Magmell's dangerous wildlife. One such angler is the highly-skilled and experienced Inyou, who performs search and rescue operations for clients with the help of his assistant, Zero.