Monarch was founded in secrecy in 1946 as a joint coalition between several governments in order to hunt and study massive unidentified terrestrial organisms (MUTOs). The first such creature Monarch studied was Shinomura, a deadly hive-minded radioactive creature composed of many smaller composite lifeforms. One of Monarch's operatives, Eiji Serizawa, also was intrigued by eyewitness accounts of a "giant lizard that walked like a man" that seemed to be chasing Shinomura throughout the islands. Serizawa called this creature "Gojira," after Pacific Island legends describing him. In 1954, Monarch cooperated with the United States military to lure Godzilla and Shinomura to Bikini Atoll, where both were thought to be killed by the Castle Bravo nuclear bomb "test". Shinomura was confirmed to be destroyed by the bomb's blast. Godzilla, however, managed to survive. Decades later, in 1981, Eiji told his son Ishiro about his experiences and belief that Godzilla was still alive somewhere. After Ishiro's father died, he was approached by Shaw, a representative of Monarch and his father's colleague, who offered him the opportunity to join the organization and continue his father's work. Ishiro Serizawa readily agreed and became a member of Monarch.
In 1973, Monarch and Landsat conducted an expedition to an island in the South Pacific called Skull Island, with William Randa, Houston Brooks, and San Lin representing the organization. At this time, the organization was nearly bankrupt. After returning from Skull Island, Brooks and Lin debriefed survivors, James Conrad and Mason Weaver, before presenting them with a slideshow, showing four ominous cave paintings, with each depicting a giant creature.
In 1999, Ishiro Serizawa and his assistant Vivienne Graham were sent by Monarch to the Philippines to investigate the cave-in of a mine. There, they discovered the skeleton of another member of Godzilla's species that died long ago and two parasitic spores, one of which had hatched. The creature that hatched from the spore arrived at the nuclear power plant in Janjira, where it attached itself to the reactor to feed. Monarch quickly quarantined the city of Janjira to study the creature, codenamed MUTO. In 2014, the MUTO burst free from its cocoon and destroyed Monarch's facilities and flew away. Serizawa and Graham then assisted the U.S. military in tracking and studying the MUTO and Godzilla once he emerged to hunt it. "The Godzilla Revelation", a featurette on home video releases of Godzilla, indicates that the world learned of Monarch's existence shortly after the events of the film, with an individual calling themselves MonsterTruth leaking classified videos and documents to the press.