When world peace is threatened by the emergence of a terrorist group called the Black Cross Army, the United Nations forms the Earth Guard League, known as EAGLE, to combat this growing danger. The Black Cross Army, led by the mysterious Black Cross Führer, launches a devastating counterattack against EAGLE's five Japanese branches, slaughtering nearly all personnel. At each of the five bases, a single agent miraculously survives: Tsuyoshi Kaijo, Akira Shinmei, Daita Oiwa, Peggy Matsuyama, and Kenji Asuka. These five survivors are summoned to a secret underground headquarters located beneath a snack shop called Gon, where EAGLE Japan's commander, Gonpachi Edogawa, recruits them for a new mission. They become the Himitsu Sentai Gorenger, a secret squadron equipped with electronic battlesuits that grant superhuman strength and speed. By shouting Go, they transform into color-coded heroes: Tsuyoshi becomes the red-clad leader Akarenger, Akira becomes blue Aorenger, Daita becomes yellow Kirenger, Peggy becomes pink Momorenger, and Kenji becomes green Midorenger.

The series follows the team's episodic battles against the Black Cross Army's schemes to conquer the world. Each episode typically centers on a plot devised by one of the army's superpowered masked agents, known as Masks, who command legions of foot soldiers. These schemes range from relatively mundane operations involving weapons development and assassination to more exotic threats like demolishing the Van Allen belt, freezing the planet, or using metal-eating bacteria to cause destruction. One notable three-episode arc involves the Black Cross Army discovering an ancient airship that sank Atlantis and attempting to use it to sink Japan.

The Gorengers operate from their base beneath Snack Gon, using various vehicles and weapons to counter the Black Cross threat. Aorenger serves as the team's pilot, flying their aircraft the Variblune. Momorenger, a skilled chemist and explosives expert, creates bombs and modifies the team's signature finishing attack, the Gorenger Storm. In this attack, the team passes an explosive soccer ball among themselves before Akarenger delivers the final kick to destroy their opponents. Each ranger wields individual weapons that pull from their visors, including Akarenger's Red Vute whip, Aorenger's Blue Cherry bow, and Midorenger's Midomerang boomerang.

Throughout the 84-episode run, the series balances spy thriller plots with deliberate absurdity and memorable action sequences. The Black Cross Army's masked antagonists feature inventive designs such as Telephone Mask, Locomotive Mask, and Poison Gas Mask. Despite the comedic elements, the series does not shy away from darker moments, including violent on-screen deaths and unsettling scenarios such as people brainwashed into becoming synchronized suicide bombers. The team faces personal challenges as well, including Peggy visiting a village afflicted by a vampire snake woman and Kenji seeking revenge against the Poison Gas Mask who attacked his base.

Midway through the series, a significant change occurs when original Kirenger actor Baku Hatakeyama leaves the show. His character Daita Oiwa is promoted to commander of the Kyushu EAGLE branch, and a replacement, Daigoro Kumano, takes over as the second Kirenger. After Kumano is killed in action, Oiwa returns to active duty with the Gorengers for the remainder of the series. The team continues fighting until they finally confront and defeat the Black Cross Führer, bringing an end to the Black Cross Army's reign of terror.