It's the athletic festival. Kakeru hurt his ankle during the pole-toppling game, and hid that fact from everyone else. Kakeru tries to keep his suffering to himself, when Suwa and the gang call out to him. Met with everybody's kindness, Kakeru begins to tell them what he's been keeping pent up inside. And then, the class relay begins.

It’s the spring of Naho’s second year in high school, and Naho receives a letter from herself, 10 years in the future. The letter accurately depicts what’s about to happen, including details on a transfer student from Tokyo, Kakeru Naruse, who ends up sitting beside her in class. On top of that, the letter also begs Naho not to invite Kakeru out with her group of friends on that day alone, but why?

It's spy vs. spy as D-Aggency and Wind Agency both race to prevent Japan's "Grand Strategy" from falling into enemy hands.

Former diplomat Shirahata Ki'ichiro is suspected to have illegally gained knowledge of the Imperial Army's top-secret "Grand Strategy." Investigating in secret, Gamou Jirou makes contact with Shirahata's old friend, the British consul Ernest Graham.

The luxury liner Tokimaru makes its way from San Francisco to Japan, stopping at each Hawaiian island along the way. As Utsumi Osamu sits on the deck enjoying a crossword puzzle, he's approached by a man calling himself Jeffrey Morgan. At that same moment, cries of terror erupt from those looking out at the ocean.

D-Agency receives an urgent meeting request from one of their collaborators, Morozoff, who has important secret information to report. D-Agency member Seto Reiji arranges to meet him on the South Manchurian Railway Asia Super Express. As Seto moves to collect the information, he finds Morozoff has been murdered.

Izawa Kazuo has a good life running a simple photography store in London... until he's suddenly arrested under suspicion of espionage. As Isawa undergoes a harsh interrogation, Lieutenant colonel Howard Marks, master spy for the British Secret Intelligence Service, appears before him.

Sergeant Honma Eiji has been assigned to the Shanghai military police. Not long after assuming his new post, he is summoned by Captain Oikawa Masayuki. Oikawa orders Honma to conduct an internal investigation and uncover an enemy agent who's infiltrated their ranks. As he explains the mission, they hear an explosion...

A man wakes up with complete amnesia. His only posession? A passport with the name "Shimano Ryuunosuke" and the port of entry, Marseille. Speaking with to Alan, the mysterious man next to him, he learns France has been occupied by the German army.

The raid of Gordon's home comes up empty. And when Gordon lets it slip that this is the second time his home's been searched, Sakuma realizes the mission is a set-up by Mutou.

Karl Schneider, writer for the Berlin Allgemeine, is suspected of being a German/Soviet double agent. While D-Agency searches for proof of his espionage activities, Schneider suddenly dies under mysterious circumstances. Lieutenant Colonel Yuuki sends his men on individual missions in order to uncover the truth.

Hermann Wolff, a Wehrmacht Colonel assigned to German's intelligence agency, the Abwehr, investigates a suspicious train crash on the outskirts of Berlin with his right-hand man, Lieutenant Johann Bauer. Among the belongings of one of the bystanders is one of a spy's standard tools of the trade. When interrogated, its owner claims to have stolen it from a Japanese man named "Maki Katsuhiko..."

Aaron Price, Far East correspondent for the British Times, investigates the true identity of Lieutenant colonel Yuuki, the man rumored to have founded D-Agency. Flipping through the Military Preparatory School's list of past enrollees, his eye is drawn to a boy who passed the entrance exam at the top of his class, but was expelled for violence. His name? Arisaki Akira.

Autumn, 1937. Against the Imperial Army's objections, Lt. Colonel Yuuki establishes the spy training group "D-Agency." The army sends Liuetenant Sakuma to serve as their liason to D-Agency, and he watches the applicants easily coast through the brutal examination process. Not long after, Sakuma is ordered by Colonel Mutou to search the home of a suspected American spy, the Japanophile John Gordon. Disguised as military police, Sakuma leads D-Agency on their first mission.

Touya arrives in Oedo, a Japanese-style castle town within Tokugawa Ieyahsu's domain, and quickly heads to Yae's home. There he meets their servant, Ayane, and Yae's mother, Nanae, before hearing that Yae's father and brother went off to war with Ieyahsu.

After returning from the Kingdom of Mismede, Touya and the others enjoy their daily life. Yet behind the scenes the women battle over the bicycle Touya created! Notice it, Touya! At Sushie's request they head to Mismede and return to find Leen and Paula. According to them, the crystal beast Touya and the others once defeated had appeared in Mismede as well, and Leen struggled to defeat it. So she began to take interest in Touya after he defeated the beast. Acutely interested in the high spec Touya, Leen asks Touya and the others to investigate some ancient ruins, leading to the start of a new adventure! (Made easier with Gate.)

Touya's party heads out for Mismede once more. Then they finally arrive in Mismede's royal capital, Berge. Their party heads to the palace and gains audience with King Jamukha. Then somehow Touya and the King end up doing battle in their fighting arena?! That night a party is held in the royal palace, but a moving stuffed teddy bear appears before Touya when he sneaks out of the reception! The bear leads him to the self-proclaimed 612 year old fairy leader, Leen. Then Touya uses his newly obtained Null magic, Program, to create the handgun Brunhild, and grow even more powerful!

After receiving a huge mansion in place of court rank, Touya and the others begin living their usual dense, thickheaded lifestyle. Then Duke Ortlinde's daughter Sushie joins them. They receive a mission to head all the way to Mismede because she'd like to use Touya's Gate spell for talks with The Kingdom of Mismede. Mismede's ambassador, Olga, her daughter Arma, and their two guards join their traveling group. On their journey they encounter a dragon attacking a village on what should normally be sacred ground! It's Touya vs another world's orthodox dragon! Which party will win...?!

Touya and the others set out to investigate some magic beasts, but it turns out their destination is the castle of a mage who researched slimes, which they'd all been avoiding (though Touya seems excited?) Touya and the others advance to carry out their investigation, but Green Slimes capable of dissolving clothes stand in their way! They climb the staircases to run away from the slimes chasing them, but in their path are Lotion Slimes! The way forward is wet and slick! The way back is slimy and smooth! What was the goal of the research behind this slick and slimy and slime panic?!

Touya is brought to the royal palace by the Duke. There he finds the King, bedridden, on the verge of death after being poisoned by someone... No one knows how to treat it, and many believe there's no hope of saving him. Yet high-spec Touya handles the poison with ease! He saves the King with his super Healing magic, Recovery, and even catches the criminal who poisoned the King quickly, bringing everything to resolution. Meanwhile, after watching Touya's actions, Princess Yumina makes a startling declaration...