Despite a rough start, Makoto Misumi's life in another world takes a positive turn when he meets more demihumans who recognize his presence. Now as the leader of a fast-growing demihuman community, Makoto wishes to make human society more accepting of them and thus builds a business showcasing the demihumans' abilities. To extend his reach further, Makoto enrolls at the Rotsgard Academy to learn magic and expand his business venture there. Meanwhile, the goddess who summoned and forsaken Makoto had brought two other people to her world shortly after sending him away, making them heroes of their respective nations. Given enough time, Makoto's path will intertwine with both of these heroes, which may cause the world to take a drastic direction.

Mage's Association members Rin Toosaka and Luviagelita Luvia Edelfelt are tasked with finding and retrieving seven Class Cards, medieval artifacts containing the life essence of legendary Heroic Spirits. To aid them in their mission, they are granted the power of Ruby and Sapphire, two sentient Kaleidosticks that would enable them to transform themselves into magical girls and drastically increase their abilities. However, the two mages are on anything but good terms, prompting the Kaleidosticks to abandon them in search for new masters. They stumble upon two young schoolgirls—Illyasviel von Einzbern and Miyu—and quickly convince them to form a contract. With their new powers and responsibilities, Illya and Miyu set forth to collect all the Class Cards.

Led by Kakashi Hatake, Naruto Uzumaki, Sakura Haruno, and Rock Lee are tasked to escort the extravagant Prince Michiru Tsuki and his spoiled son Hikaru to the prosperous Land of Moon when the two return from a long trip around the world. As if guarding two whimsical high-ranked individuals was not challenging enough, the prince's reckless decision to acquire an entire circus during their journey—mainly to entertain Hikaru's wish of owning the saber-toothed tiger featured in the show—further propels the mission into disarray. Just as things are finally settling down, the arrival of Michiru's convoy at the Land of Moon is met with an unforeseen crisis—the greedy Chief Minister Shabadaba has taken over the country with the assistance of mysterious, powerful ninjas. While Kakashi's team relentlessly fights the enemy by any means necessary, the two princes are forced to confront a new outlook on life through adversity.

In Fuyuki City, the Fifth Holy Grail War is about to commence a lengthy battle of blood, death, and misery. High school student Rin Toosaka has trained her entire life for this moment—to become a magus capable of being a Master in the war. Summoning her Servant known as Archer, Rin finally sets foot into the battle. Discovering that one of her acquaintances, Shirou Emiya, is drawn into the war as well, Rin offers to form an alliance for the time being. And as the two of them grow closer, Rin begins to learn more about Shirou's fate and ideals. Nevertheless, her goal remains the same: to win the all-powerful relic that can fulfill the wishes of those who are victorious after the war—the Holy Grail.