Following the defeat of a great adversary, Gokuu Son and his friends live peaceful lives on Earth. Meanwhile, in space, Beerus the God of Destruction awakens from his long slumber, having dreamed of an entity known as a Super Saiyan God. With the help of his assistant, Whis, Beerus looks for this powerful being, as he wishes to fight a worthy opponent. After discovering that the Saiyan home planet was destroyed, he tracks down the remaining Saiyans on Earth, looking for Gokuu specifically. Having only heard of the Super Saiyan God in legends, Gokuu and his comrades summon Shen Long the Eternal Dragon, who they find out is afraid of Beerus. After learning the secret of the Super Saiyan God, an intense battle between Gokuu and Beerus commences, the immense power of which puts the Earth in terrible danger.

Unleashing a devastating surprise attack, flying ninjas from the Land of Sky are seeking revenge against their old enemy Konohagakure. Despite his eagerness to join the fight, Naruto Uzumaki is held up by Shinnou, a mysterious doctor who requires his assistance to save an injured person. While delivering the wounded man to the hospital, Naruto has an unexpected encounter with Amaru—a stormy youngster from a neighboring village desperately looking for Shinnou's help. Meanwhile, as the invaders withdraw to restore their forces, Tsunade seizes the opportunity to dispatch a small team including Sai, Shikamaru Nara, and Kakashi Hatake to strike down their base. Simultaneously, she commissions Naruto, Sakura Haruno, and Hinata Hyuuga to accompany Shinnou and Amaru on their journey. During this time, however, Orochimaru has his own schemes: he orders Sasuke Uchiha to bring him the doctor who specializes in the reincarnation technique. As the escort group accidentally uncovers the sinister truth behind the attacks, tumultuous plans are set in motion. But even when confronted with an unforeseen reunion, Naruto does not waver in his endeavor to end the warfare and its disastrous effects.

Throughout Shibuya, a series of murders dubbed the New Generation Madness gained widespread attention As these crimes gained infamy, they became a hot topic of discussion among the people of the area. Nonetheless, these New Gen murders do not capture the interest of Takumi Nishijou, a high school otaku who frequently experiences delusions and feels that he is constantly being watched. Having no concern for the real world, Takumi spends his time playing online games and watching anime. However, his ordinary life is disrupted when he receives a horrifying image of a man staked to a wall from a user named Shogun. After calming himself at an internet cafe, Takumi sees the exact same murder scene as the image portrayed happen right before his eyes, along with a pink-haired girl covered in blood calling out his name. Conflicted with the nature of reality, Takumi finds it difficult to judge where to place his trust as he gets caught up in the New Gen murders, believing that the murderer is out to get him.

Led by Yamato, Naruto Uzumaki, Sakura Haruno, and Sai are assigned to capture Mukade, a rogue ninja who is pursuing the ancient chakra Ryuumyaku located underneath the Rouran ruins. While the Ryuumyaku has been sealed by the Fourth Hokage, the group fails to prevent Mukade from releasing its power. Consequently, a strong energy burst engulfs both Naruto and Yamato before they can escape. As he awakens in a magnificent yet hostile kingdom, Naruto meets its young queen Saara and three Konohagakure ninjas on a top-secret mission. They reveal to him that he has time-traveled to Rouran 20 years into the past! To make matters worse, Mukade has already infiltrated the royal court, becoming the naive queen's most trusted minister under the alias Anrokuzan. Joining forces with the three ninjas, Naruto must protect Saara's life without fail to stop the villain's plans and return to the present.