A scholar and his student disembark to a small area in the Tohoku region to gather research concerning the natives' mountain god: Baradagi. However, during their expedition, they stumble upon the root of the natives' lore: a giant, spike incrusted, monster called Varan, who quickly kills both of the researchers. The creature then moves on and wipes out the nearby Iwaya village before submerging underwater.

It isn't long before word of the monster reaches the Japanese government, and an Anti-Varan Headquarters is established by the Ministry of Defense. Meanwhile, Sugimoto, a biology professor, concludes from his research that this monster is a Varanopode, a creature which lived some 185 million years ago. An expert in the field, the Ministry of defense quickly enlists Sugimoto's aid after his discovery, and he joins the attack squad being positioned near the Tohoku region.

Once fully mobilized, the military wastes no time in beginning their assault, as they shell the nearby lake with toxic chemicals to drive out the beast. Varan responds to the attack, emerging from the surf as nearby tanks and rocket launchers unload a volley of shots at the creature. The attack proves ineffective, though, as Varan begins to march through the defense lines. During the creature's raid, a nearby tree is toppled over and Yuriko, a reporter, is caught underneath it. Kenji, one of Sugimoto's aids, arrives just in time to save the girl from the monster's advance. The pair runaway and take shelter in a nearby cave, while Varan remains in close pursuit and blocks off their exit. Professor Sugimoto, running off a hunch, advises the military to fire their flares toward the mountain to distract Varan. The professor's hunch proves to be well founded, as the creature leaves the mouth of the cave and climbs the mountain where the flares were fired. However, unexpectedly, Varan raises his arms to reveal large flaps of skin which the monster uses to glide away from the mountain and into the ocean.

Varan quickly swims through the current and arrives near Haneda airport, in Tokyo, by nightfall. Having evacuated the area, the military prepares for another confrontation with the monster, as nearby battleships, tanks and jets all focus their attacks on the creature. As before, though, the conventional weaponry has no effect. Fortunately, the military has one final means of attack, and begins to prepare a large quantity of Special Gunpowder, a powerful new explosive, to utilize against the creature. Kenji makes the first strike: driving a truck laced with the explosives near the monster, which is then detonated as Varan approaches it. Once again, though, the attack proves unsuccessful. The professor, falling back on his earlier hunch, requests that the military launch a light bomb into the sky, filled with the Special Gunpowder set on a timed fuse. The request is fulfilled, and Varan acts as Sugimoto had hoped, eating the flare while its in mid-air. The creature is then rocked with an explosion that hits from inside, as Varan retreats back into the water. He is too late, though, as a final explosion detonates from his own body, destroying the creature.

The original version of Varan (1958), this project started as a made for TV film that was being produced by Toho and AB-PT, a division of ABC, following the success of Toho's kaiju pictures in the US theatrical arena. For the movie, Toho reunited most of the key players who worked on Rodan (1956), including director Ishiro Honda, producer Tomoyuki Tanaka, writer Shinichi Sekizawa, special effects director Eiji Tsuburaya, and composer Akira Ifukube. The film was intended to be shown through ABC for American audiences, and Toho constructed the picture accordingly: filming in black and white and on a full screen, 1.33:1, aspect ratio.

However, like Latitude Zero (1969), the US backing for the project fell through. When this occurred, though, Toho had already finished most of the film. Ifukube's score was ready to go and most of the principal shooting was already completed. Consequently, Toho then prepared to adapt Varan for a theatrical release in Japan, instead of throwing away the work and money that had already been spent on the project. To do this, Toho had the writers draft another screenplay, adding many new segments to the film. These segments included the early side plot with the butterflies and the struggle with the Iwaya villagers, while rewriting most of the scenes involving dialogue. More special effect shots were commissioned as well, including the lengthy water battles seen in the final product. Ifukube was also hired to re-score the film, allowing the composer to reconstruct the score utilizing a bigger orchestra, while also composing music for the added scenes.

Despite Toho's continued commitment to the project, though, several problems arose in adapting the movie. The most apparent being that the film had to be completed in black and white to match the footage that had already been done, while Toho had been doing color special effects movies since 1956 with The Legend of the White Serpent. The other was that the film had to be prepared to be shown in a Toho Scope, 2.35:1, aspect ratio, while the already completed footage was shot at full screen. To solve this dilemma, the already completed footage was cropped greatly in order to match with the new scenes.

The newly completed film was released in Japanese theaters on October 14th, 1958; however, fascination with the film's troubled production lived on in the decades to come. In 1996, Ifukube's score for the televised version of the film was released by Futureland as additional tracks on their Varan CD. In 2005, Toho released Varan on DVD, including the televised version as an extra. As expected, the feature was incomplete, with some footage missing, although most of the audio had been recovered. The feature also revealed that the film was intended to be a mere 54 minutes in length, while also being broken down into two smaller episodes, each 26 minutes in length. Sadly, the footage was cropped for a 2.35:1 aspect ratio, instead of the TV version's original full screen dimensions. This feature was also reprinted on Tokyo Shock's 2005 release of the movie under Varan the Unbelievable.