Deep in a tropical jungle, young Yaiba Kurogane diligently practices swordsmanship alongside his father, Kenjuurou, completely unaware of the modern world. However, one day, the two end up in a container on its way to Japan. There, they encounter Kenjuurou's old rival, Raizou Mine, and his daughter, Sayaka. Out of other options, Yaiba agrees to a deal with the Mine household: if he beats the strongest student in their dojo, he will be welcome to stay. Using his distinctive skills and extraordinary strength, Yaiba earns his place. Wanting to fight more powerful enemies, Yaiba follows Sayaka to school—where he quickly loses to Takeshi Onimaru and acknowledges him as his new rival. With Onimaru inheriting the sword of his bloodline and obtaining demonic powers, Yaiba must train to become even stronger and beat him for good.

Hu Bayi and his companions, commissioned by Professor Chen, travel to Coral Temple Island in the South China Sea and hire Ruan Hei and his apprentice to embark on the Trident to search for the Qin Emperor's Bone Mirror. After their adventure, they crash into Guixu, where they discover the ancient mirror within the shipwreck and learn that Ruan Hei is Duoling's enemy. While resting after their escape, a mysterious figure suddenly appears, wielding a club, approaching Uncle Ming, who is on night watch.

Hikari is a girl whose mother Mari has fused with a spaceship. Traveling in the spaceship, Armadillo, Hikari experiences things and encounters people, including a strange boy called Romeo who emerged from the extracted noise she came across on the Web, and her long-lost father Raven.

Masou Gakuen HxH specials included with the volumes of the DVD/BD.