In the year 2048, a large mechanical sphere falls from space and starts attacking major cities around the world. After much destruction, the sphere hovers over the jungles of South America, drawing lines into the ground as it expands and draws energy from the jungle foliage. Equipped with its own defense system, the Sphere destroys all attacks made on it by Earth's military.

The original Aleste fighter ship's failure to stop the sphere's growth prompts the construction of a space fighter capable of wielding amazing weaponry, that fighter being the Super Aleste. Tasked with flying into and destroying the sphere, the Super Aleste must also destroy any reinforcements the sphere calls for which come from the deepest depths of space.