After the conclusion of the Second World War, General Robert Savage spoke to the newly formed United Nations, and stressed the importance of not only a world diplomatic force, but a policing force. The General is placed in command of the UN's security forces, which were named G.I. Joes by the public. Joe gradually gained power, taking over world security and gradually using their influence to first sway, then dictate, policy on a global scale. Temporary emergency powers become permanent, and the scale of Joe operations kept growing. Under the Joes, peace was maintained and strengthened, and even though there are still seeds of discontent, the Joes faithfully and honorably defend the principles of justice and security, if not liberty.
Of course, there are those who see things otherwise, and feel the Joes are an excessive jingoistic overreaching arm of the United States, enforcing its foreign policy at the expense of the rest of the world. To some, Cobra are heroic freedom fighters, battling against the odds in the name of true freedom from the Joes' worldwide police state.
In 1982, Joe science teams uncovered an alien spacecraft and studied it, which gave them a huge technological edge. They use this edge to enforce their will across the world. Discovering ancient alien robots in the Ark, the Joes did they best they could with limited technology to bring them back to life. A few were repaired and given new Joe vehicle altmodes. However, not all of the bots repaired were Autobots, and many of the Decepticons immediately left the Joes to seek their fortunes elsewhere. One of them, called Megatron, gathered some of the others and built an undersea base, far away from prying human eyes...
In 1986, a few of the Autobots managed to contact Cybertron, and requested reinforcement to assist G.I. Joe in providing security to planet Earth. That same year Sparkplug reluctantly committed Spike to Seattle Memorial Psychiatric Hospital, where he stayed for almost seventeen years.
In 2002, Sparkplug checked Spike out of Seattle Memorial Hospital and assigned him to help with assimilating the Autobots into Earth's culture. The work arrangement worked beyond the Joes' wildest beliefs. Spike struck up a natural friendship with the Autobots like no other human before him, and Spike's new sense of purpose led him to slowly wean himself off the bevy of psychiatric meds prescribed to him. Even with these strides, Spike is still painfully shy and withdrawn, opting to spend all of his time at work. Sparkplug routinely finds himself assuming a caregiver role for Spike, be it talking him through his many panic attacks, or kindly teaching him how to drive.
In 2005, the first Junkions arrived on Earth, seeing out the source of intercepted TV signals. Later that year, a massive planet-eater named Unicron attacked Cybertron, looking for something it called the Matrix. Not finding it, Unicron destroyed and consumed the planet, leaving only the Transformers on Earth and other planets alive. For the next several years, Unicron heralds have scoured the cosmos, looking for the Matrix.
The Joes recruited retired G.I. Joe spy Sparkplug Witwicky to lead the ongoing Ark Project. Sparkplug was tasked with the duty of bringing back the remaining offlined Autobots and assimilating the awakened Autobots into Earth's culture. Sparkplug isn't the only Witwicky to work with the Joes. Sparkplug's youngest son, Buster, was recruited while he was still in college to be a computer code cracker. In the early '80s, Susan Witwicky (also an undercover Joe agent) was killed by an unknown assailant in front of Spike, the eldest son of Susan and Sparkplug. That event traumatized Spike to the point where he became extremely depressed and eventually suicidal.
For years, Buster worked on improving the G.I. Joe infrastructure. However, he slowly grew disillusioned with his job as he was asked to repeatedly perform tasks that he felt were in strict violation of peoples privacy. While maintaining a cover for G.I. Joe, Buster occasionally worked as a columnist and cartoonist. This led to repeated confrontations with Duke. The job began to wear Buster down to the point where he grew isolated and according to some of his friends, excessively paranoid. The stresses of his job eventually led to Buster's longtime girlfriend Jesse leaving.
In the Joe world universe, General Flagg and Lieutenant General Hawk leads a worldwide peacekeeping force called G.I. Joe. They are assisted by their XO, Brigadier General Flint, who oversees the Ark Project. The Ark Project recovers and rebuilds damaged Autobots into G.I. Joe vehicles. With Optimus Prime as yet unrecoverable, the Autobots on Earth defer to General Hawk. Duke leads field operations around the world.