In the year 199X, four meteorites crash into the Earth and leave the city of Tokyo in ruins. In the wake of the disaster, the only things left standing are four enormous crystal towers. After the horrific ordeal, scientists are sent to study the giant objects. The crystals are virtually impossible to remove or be destroyed. Later, scientists eventurally conclude that the objects pose no threat and a decision is made to rebuild the city around the crystal towers. Little do the people know that the towers are actually a gateway to another world where a powerful alien force is plotting to take over the Earth.

Fast forward to the year 202X. A beautiful young lady named Memory Gene and her team of scientists have created the Borgman (singular and plural like Jedi) - a race of cybernetic humans designed to conduct future missions for the world space program. The first two candidates to successfully become Borgman are Ryo Hibiki and Chuck Sweagar.

During the final stages of the Borgman project, the science facility is attacked by Gilbert Mesh, a former colleague of Memory's who acquires supernatural abilities as a result of his connection - unknown to the Borgman - to the mysterious crystals that fell to Earth. Weakened by the attack, the ceiling collapses on the capsules that contain future Borgman.

After Mesh's surprise assault, Memory focuses her efforts on protecting the Borgman against future attacks. A new Borgman headquarters is constructed beneath an elementary school where Memory, Ryo, and Chuck take jobs in order to conceal their identities from Mesh and his army. There, Memory assumes the role of the school principal while Ryo and Chuck pose as ordinary school teachers. From their new underground fortress they monitor the city with advanced computers and equipment in order to ensure everyone's safety.

A third Borgman, Anice Farm, joins the team after a near-fatal car crash leaves her hovering on the brink of death. Unlike Ryo and the other candidates who willingly volunteered to become cybernetic beings, Anice was made a Borgman without her prior consent. After Anice recovers from the surgery, Memory explains what happened to her and that the procedure was her only hope of survival. Memory then asks her to join the Borgman team. Grateful to be alive, Anice accepts Memory's offer.

The year is now 2030. Memory and her Borgman are put to the test when Megalo City's main power facility in Tokyo Bay is infiltrated by a secret and sinister organization.

With aid from five battle-suited female cops called Phantom S.W.A.T., the Borgman confront a legion of supernatural beings identified as "Youma." Our heroes soon find themselves in a race against time to defeat an unpredictable enemy and discover the identity of a mysterious Borgman named Dust Gead. - Jeff Anglea