On a relaxing autumn day, Shinonome High School was bustling with activity for the upcoming school festival. Mr. Fujisawa, an avid mountain climber and teacher, patrols the school grounds. The entrepreneurial Nanami is working hard to sell boxes of lunch. Jinnai, the class president is neck deep in a scandal. Makoto is completely absorbed in his invention. The whole day seemed as if it would end peacefully, when a problem occurs. Jinnai, who is unjustly resentful of Makoto, decides to interfere with Makoto's invention causing it to run amuck. The machine makes a humming sound and sends Makoto and company to another world. To the magnificent world of EI-Hazard! What fate awaits Makoto, Jinnaii, Fujisawa sensei, and Nanami!?

Makoto, lost in this mysterious world, accidentally, meets up with Fujisawa sensei who was transported to a near-by location. With no knowledge of what lies to their left and right, in their past and their future, the two ponder of ways to get home. When the pair rescue a young girl from Bugrom, the insect people, they are invited to the palace. The young woman the twosome rescued happened to be Rune Venus, the princess herself. Although treated as guests at first, they arouse suspicion when Fujisawa sensei demonstrates his superhuman strength. Without any clue as to how return, the night passes...

Time merely passes by the pair of Makoto and Fujisawa sensei, without any ideas to how to return to their world. In the meantime, Jinnai becomes completely buddy buddy with the queen of the insect people, Diva and declares his eventual conquest of EI-Hazard. The two parties end up meeting on opposite sides of a water dispute in a village.

Makoto and company set out on a quest to find the three priestesses who have knowledge of "the ancient power." On the way, they encounter interference from Jinnai and the Bugrom but, eventually, arrive safely at the Temple of Water. There, the High Priestess Meeze falls head over heels for Fujisawa sensei. Could this be the creation of a cross-dimensional couple!?

Makoto and company's next goal is to seek out High Priestess Afura of the Temple of Wind. However, as soon as they arrive, they are mistaken for carpenters and are charged with the undertaking of constructing a summerhouse. They will be permitted to enter the temple's library upon the completion of the summerhouse. The construction progresses undaunted by failures and complaints!

Makoto and company encounter a girl on the way to the Shrine of Fire. When asked, she reveals that she is the High Priestess Shayla-shayla. In order to help her and help her retrieve her temple which she lost in a bet, the duel begins between Makoto and Jinnai.

Lost alone in a strange world, Nanami works a part-time job. When her cooking using soy sauce becomes a hit, she becomes financially independent. As she drags her cart about selling bento, she reaches the Temple of Water. There she meets Meeze...

In order to convey her feelings for him, Meeze travels to Roshtaria to see Fujisawa sensei. However, her efforts meet with little success. In the meantime, Nanarni is left in charge of the temple and opens it up for business when she decides to turn holy ground into a giant amusement park!

Things at the palace settle down after Makoto and company are reunited with Nanami. However, soon after Nanami vanishes. It is obviously the work of Jinnai and the Bugrom but, they have no evidence to prove it. Makoto is shaken and loses confidence in himself, nonetheless he becomes driven to solve this puzzle.

Returning from investigating some ruins, Makoto and company pass by a village somehow end up taking on the job of ridding the village of its terrible monster. When the crew enters the jungle they meet a cat-like creature. They decide to name it Oolah and with its help, try to come up with a plan but...!?

At the request of Princess Rune, Makoto and company help construct an orphanage. spite the fact that they've taken on an unfamiliar role, things seem to be going ell, when an orphan named Milly runs away. And unbeknownst to the crew, Jinnai's plan is already in motion.

Roshtaria is suddenly taken siege by abnormal weather and a sudden groan from the earth is accompanied by the appearance of a floating castle. According to myth, a demon is sealed within its walls. Makoto and company struggle to prevent the demon from being unleashed but to no avail, the seal is broken.

The demon Ifrita awakens and becomes one of Jinnai's minions. With the ultimate weapon under his command Jinnai demands unconditional surrender from Roshtaria. He attempts to attack with Ifrita but... All the ultimate weapon does is create a comedic mess.

In order to unveil the mystery of the snow which is said to fall every several hundred years, Makoto and crew decide to join an investigation party. Jinnai hears of this and along with Ifrita attacks them in order to steal the snow away from them. However, the snow, itself, refuses to give up any of its secrets.

The Fire Priestess Shayla-shayla and the Wind Priestess Afura Mahn, as talented as the two are, their bickering never ceases. The two seem to share an interesting past. A story which is about to be revealed.

A large tornado approaches the palace of Roshtaria. The tornado is, in fact, Ifrita who has lost control over her powers. As the Priestess of Wind, Afura tries to stop the rampage but, is unsuccessful as is Shayla. And the tornado continues its approach towards the palace...

Makoto learns from the princess of an ancient royal room named the Room of Contracts and together head there. There they encounter numerous, mysterious murals and an interesting development... When the terms of the lore are fulfilled, the stairway to heaven shall appear!

With no end in sight of the war with the Alliance, Jinnai loses his patience and decides to put into action his plans to kidnap Princess Rune Venus. The evil hand of the odd couple of Jinnai and Ifrita threatens the princess at the memorial ceremony in the Balm Kingdom. What fate awaits the princess!?

Jinnai who successfully kidnaped Princess Rune hurries his way back to the Bugrom Castle. Makoto and Fujisawa do their best to catch up with them. But Daiseiga obstructs the road and the kidnapper gets away. What did the princess see in the castle Bugrom?

Captured, yet happy-go-lucky, Nanami makes friends with her enemy in the castle of Bugrom. Rune become friend with Ifurita. When a quarrel between Jinnai and Nanami grows to it's worst point, some-unexpected things occur.

Makoto sets of to Bugrom territory to save Rune and Nanami. In order to get to the Bugrom territory, Makoto has to cross "the sacred river". Makoto and his buddies have to face man an ordeal on the evil route. Where does a girl's heart go in the battle?

Makoto and friends finally reach Bugrom territory. While Meeze and Fujisawa battle with enemies, Makoto and Shera continue their journey to the castle where Rune is confined. Ifurita and Shera battle while Makoto and Jinnai fight a man-to-man fight over Rune.

Though freed from Jinnai and Bugrom territory, Rune and Nanami lose sight of heir Comrades. They are on the run but they don't know their way. Their confidence in each other grows as their journey and battle with pursuit continues .

Jinnai is enraged by the fact that he couldn't stop Runes escape. As his last resort, he plans to use the "eye of God" to make a general attack on Roshtaria. The "eye of God unleashes all kinds of natural disasters on Roshtaria. Jinnai demands the total surrender of Roshtaria. The war reaches ifs final stage.

A change occurs within Ifurita, while manipulating the "eye of God" and she turns into her previous self Ifurita attempts to destroy El-hazard. Makoto and Rune are the only two who have the power of "kings seal" to stop a rampage of the "eye of God".