Eight years after a great war was waged between colonies in outer space, peace has finally settled back onto the Earth. Tadashi Himukai, a 17-year-old war orphan, purchases a used worker-mech in order to start a construction business with his girlfriend, Elina Furfa. However, when he first activates it, the worker-mech disguise falls away, revealing a combat model Metal Slader, which were all supposedly dismantled after the war, and an enigmatic message is displayed in the cockpit: "EARTH IN PERIL... SEEK THE CREATOR". Prompted by this warning, Tadashi, his sister Azusa, and Elina head out into space to find the answers behind it.

The story is set in 2062, eight years after a great war between space colonies. The player takes on the role of Tadashi, a heavy machines operator based on Earth. After buying a worker mech for his business with his girlfriend Elina, they discover it is actually a "Metal Slader", a military grade mech used during the war. The machine holds a secret message saying Earth is in danger and to seek the "creator". Tadashi, Elina and his younger sister Azusa decide to fly to the nearby space stations and colonies near Earth and the Moon to investigate the mech's origins and the meaning of the strange message.

Tadashi and crew soon learn that their Slader is a particularly powerful one-of-a-kind model named "Glory" and Tadashi's deceased father was its former pilot. As they continue to search for who may have designed or built Glory, a shape-shifting alien infiltrates their ship and kidnaps Azusa. In their search for Azusa and solving the mysteries of Glory, they discover a secret organization of Slader pilots that had worked with Tadashi's father. Catty, one of the leaders of the organization, explains that they were founded by a now deceased Slader designer. She also explains how the war from eight years ago was not fought between colonies but with extraterrestrials; the colony rebellion story was a cover-up. Because the aliens have the ability to take on the appearance of humans and infiltrate society, the Slader pilots prefer to stay a secret organization away from the potentially compromised government. She continues, saying that they will soon launch an attack on the aliens, and want Tadashi to participate as only he can pilot Glory. Tadashi agrees, but first they set off in search of Azusa.

Tadashi, Elina, and Catty travel to an abandoned colony to search for Azusa. After combating with several aliens, they find Azusa alive and lodged in a ventilation shaft. As they return to the secret base, they learn its location has been compromised. They escape on a large ship and prepare the Sladers for battle. Tadashi pilots Glory in a battle with the aliens and is ultimately successful at destroying their ship and saving Earth.