The Metal Slug storyline stretches from the beginning of the era of modern-day terrorism, set in the near-future of 2028. There are two militant factions that struggle for power: the Rebellion and the Regular Army. The Regular Army is a well-equipped, modern-day force run by various nations around the world. The Rebellion is comprised of various small, organized militant groups, ranging from terrorists to splinter groups of military forces driven by a hunger for power.

The Regular Army is a very formidable force. However, it lacks effectiveness due to the widespread corruption within the chain of command. Other officials often deny the reports and recommendations given to them by intelligence officers. This often leads to intelligence failures that result in dramatic consequences.

Vice Admiral Donald Morden of the Regular Army Marine Corps is one of the main characters that sparks the events of Metal Slug. He has a reputation of being a tough, efficient, and caring officer of the Regular Army, and is held in high regard by his troops. He is also a caring father to his son. However, Morden immediately defects over to the Rebellion when his son is killed in the Central Park bombing caused by an intelligence failure on the part of the Regular Army. He self-promoted to General.

In 2026, a year after the attempted assassination of the President of the United States launched by the Rebellion under General Donald Morden's command, the Rebellion launched a massive attack against the Regular Army forces around the world. Although the Regular Army intelligence agency had many indications that such an attack was imminent, Regular Army officials again ignored the warnings. With the Regular Army forces surprised, the Rebellion nearly annihilated them with their superior numbers and emergent technologies.