A scientist named Zen Shiratori was investigating the ruins of an ancient Mayan temple, convinced that the proof of the existence of a parallel world lies there. He found a strange glowing orb, which was later accidentally discover by his fourteen-year-old son Gen, who was rummaging through Dad's collection. As a result, Gen was indeed teleported into a parallel world. There, he meets a young girl named Rinna, who tells him that he is, in fact, "Gen-Kaiser", the much-expected savior of their world. Piloting giant combat robots, the two must protect the innocents of that world and defeat evil.

Kisō Shinden: Gen-Kaiser is a turn-based strategy/RPG hybrid (what is commonly called in Japan a "tactical RPG"). There is overworld navigation, and the player can also visit and explore cities; however, these features are rather rudimentary, and hostile areas cannot be explored in real time and are presented as large-scale strategic battles. The characters move in turns over the top-down battlefield and attack when enemies are in range. Animations are displayed for each attack, and experience points are awarded for successful elimination of an enemy.