The J.S.D.F. saw action in 1954, when the monster Godzilla first appeared and attacked Tokyo. Despite the J.S.D.F.'s efforts, they were unable to defeat the monster and Tokyo was devastated by Godzilla. In the following years, the J.S.D.F. would fight repeated battles against Godzilla and other giant monsters like Anguirus, Varan, Rodan, and Mothra. In order to combat these monster threats, the J.S.D.F. developed powerful new weapons, the most famous and effective one being the Maser Cannon.
Following the first Godzilla's death in 1954, the J.S.D.F. rarely saw action over the next 30 years. Amid tension from the Cold War and the threat of nuclear warfare, the J.S.D.F. secretly constructed the Super X, a powerful hovercraft designed to defend Tokyo in the case of a nuclear emergency. In 1984, when Godzilla returned to ravage Japan, the J.S.D.F. was mobilized to defend Tokyo using power Godzilla decimated the forces, forcing the Super X to be deployed. The Super X proved effective at combating Godzilla at first, but was destroyed when Godzilla toppled a building onto it. Following Godzilla's imprisonment in Mt. Mihara, the J.S.D.F. began to heavily re-arm in the likely event of his return. The J.S.D.F. created powerful electrical ray tanks called Maser Cannons and also created the powerful Super X2 from the remains of the original Super X. The J.S.D.F. also began a bio-weapons program using G-Cells collected from Godzilla in order to create the Anti-Nuclear Energy Bacteria (ANEB). When Godzilla did emerge from the crater of Mt. Mihara, he demolished the J.S.D.F.'s forces, including the Super X2. The ANEB proved to be effective in weakening Godzilla, which led to a draw in his battle with the monster Biollante. Godzilla retreated deep underwater to recover from the ANEB and disappeared for over two years. Godzilla ultimately absorbed a nuclear sub and recovered from the ANEB, growing to 100 meters tall in the process. Over the next few years, the J.S.D.F. would be confronted with other monsters, including King Ghidorah, Mothra, and Battra. In 1993, the J.S.D.F. collaborated with the anti-Godzilla branch of the United Nations, the United Nations Godzilla Countermeasures Center (U.N.G.C.C.), to form a military organization known as G-Force. G-Force soon replaced the J.S.D.F. as the primary means of fighting giant monsters that threatened Japan.
After repeated attacks by Godzilla over the years, the J.S.D.F. turned anti-Godzilla operations over to an agency known as Crisis Control Intelligence (CCI), led by Lieutenant Mitsuo Katagiri.
Following Godzilla's devastating assault on Osaka in 1996, the J.S.D.F. created a special branch called the G-Graspers dedicated to combating Godzilla. The G-Graspers developed a powerful miniature black hole gun called the Dimension Tide, intending to trap Godzilla in a black hole. During a testing of the device, a Meganula entered through the black hole and laid an egg which hatched into an entire Meganulon colony. The colony absorbed Godzilla's DNA and transferred it to their queen, Megaguirus. After Godzilla fought and killed Megaguirus in Tokyo, the Dimension Tide was fired at Godzilla, apparently successfully trapping him. Eventually, it is discovered that the Dimension Tide only buried Godzilla deep underground.
The J.S.D.F. was credited with the destruction of Godzilla in 1954 and did not have to fight any real battles in the following half century. However, the recent attack on New York City by another giant monster has put the J.S.D.F. on alert. Soon, Godzilla himself returns to seek vengeance on Japan. The J.S.D.F. was deployed to stop the monster, but was easily destroyed by Godzilla's furious power. Thankfully, the three guardian monsters Baragon, Mothra, and King Ghidorah emerged to save Japan. With the assistance of the J.S.D.F., especially Admiral Taizo Tachibana, Godzilla was seemingly destroyed and Japan was saved.
Following the attacks on Japan by Godzilla, Mothra, and Gaira, the J.S.D.F. formed a specialized branch known as the Anti-Megalosaurus Force (AMF) to combat giant monsters. Using the salvaged skeleton of the first Godzilla, AMF created Kiryu, a powerful bio-robot designed to battle the new Godzilla. Due to its Godzilla DNA, Kiryu initially ran wild and attacked AMF forces. After Kiryu's systems were repaired, it was deployed against Godzilla and fought him to a standstill.
The AMF repaired Kiryu following the battle, but was warned by the Shobijin to return the first Godzilla's remains to the ocean. When Godzilla appeared in Tokyo, Mothra herself came to fight him off. Kiryu was sent to assist Mothra and after a long battle managed to subdue Godzilla. Kiryu was ordered to finish Godzilla, but defied its programming again and chose to take Godzilla with it back to the sea.
As giant monster attacks in Japan became more common throughout the 20th century, the J.S.D.F. proved ineffective against the increasing threat. The nations of the world formed the Earth Defense Force (EDF) to combat the monsters and protect every nation on Earth.