In 1945, World War II abruptly ended when an alien race appeared on Earth and began to slaughter the human population. The year is 1999 - 54 years later, mankind is still fighting to survive against the alien forces. Earth forces now use advanced mecha called Humanoid Walking Tanks (HWTs) to combat the invaders, but throughout the ordeal, far too many pilots have been killed in action. As a result, high school students are now recruited to become HWT pilots. Gunparade March follows the lives of the 5121st Platoon, who have just added a mysterious girl named Mai Shibamura to their ranks.
