The year is 1941. In Manchuria, China, a train is boarded by Japan's Kanto Army under GENERAL SHINKAI, looking for Dr. Takamura and his "black box," when a group of mysterious ALIENS descends from the sky. Takamura's young son, TAISHI, escapes with the box to find himself cornered by the Kanto Army and the aliens... suddenly a giant robot appears to save him -- this is the Kishin Corps and KISHIN THUNDER!

The Kanto Army has Taishi's module and in an island fortress is nearing completion of their own fearsome Kishin robot to serve Shinkai's mad plans for world domination. But during testing, a use of the module causes the aliens to appear, an opportunity for the Kishin Corps to attack with Kishin Thunder. the amphibious KISHIN DRAGON and the airborne KISHIN WIND ... the battle is on!

When the Kanto Army transports their half-completed robot on a camouflaged train, Kishin Corps uses their KISHIN EXPRESS to ambush them along a stretch of double track. Suddenly another train appears headed straight for the Kishin Corps, while bombers attack from above. Can the Kishin Corps find the only way out?

July 1943. The Kishin Corps must aid in the ESCAPE of the world-famous physicist "Professor Albert" from Switzerland to the U.S., where he is to play a critical part in initiating atomic research. The escape runs into a major obstacle however, in the form of the Nazis own new robot -- PANZER KNIGHT!

Taishi's friend Jack, seeking revenge on Maria Braun for her betrayal and the destruction of the children's hideaway home in the second episode (actually the actions of her twin sister, Eva), steals the fourth module. The Kishin Corps and the Kanto Army locate the CONTROL MODULE simultaneously, and a fierce BATTLE between Kishin Thunder and Panzer Knight rages through the city, while the aliens'strange relationship to the modules becomes clearer.

Hitler has cemented an alliance with the aliens. On Rugen Island in the South Seas, which seems to the nexus for the appearance of the aliens in our world, the Nazis have built a SECRET BASE for the mass construction of Panzer Knights. The Kishin Corps heads for Rugen, but the U.S. plans an attack of its own with "Glamour Girl," a prototype atomic bomb.