The event takes place in 2636, when an alien army known as Red Falcon unleashed a massive worldwide attack on the planet by deploying their own military units from the start, in contrast to the more stealthy approaches they took during their previous two invasions in 2633 and 2634, where they took over and brainwashed local armies in order to do their bidding.
Peace was not secured at the end of the war, though, as it brought several repercussions, like yet another invasion attempt two years later, in 2638, by a branch of Red Falcon leaded by an entity known as Black Viper; and local armed conflicts by opposing organizations who were able to acquire alien cell samples during the hostilities of the war, with each group wanting to research and apply their technology for military uses, always in search to perpetuate themselves in power.
However, it was later revealed the Red Falcon army's prime directive was not actually to invade and conquer Earth, but instead they were just a defense mechanism left by an advanced tribe of omniscient beings known as the Moirai, who programmed them in order to protect and retrieve one of their most valued artifacts should it be taken from their shrine on Jupiter: the Moirai Relic.
Stealing the relic and bringing it to Earth was part of a meticulous plan devised by the Triumvirate —a group conformed by three old men who had acted as the planet's highest level in the government for centuries— with the intention of using its power for their own self-indulgent purposes and thus immortalize themselves as supreme beings. Throughout the unfolding of these events, they ended up blaming Contra commando, Bill Rizer, one of the heroes from the previous invasions, for a weapons accident that cost the life of 80% of Earth's population; in addition, he was also falsely accused for the death of his fellow brother-in-arms, Lance Bean. As a result, Bill was sentenced to a 10,000 years confinement in cryogenic stasis.
Lance was still alive, though, and after learning of the Triumvirate's real motives, he gathered a new army and declared war against Earth's established government. Looking themselves being militarily surpassed, the three old men ordered to put Bill out of cryogenic sleep to confront them, with the intention of buying them enough time until they managed to finish researching the relic and unleash its power. However, in the end it happened to be much greater than expected, and unable to control it, it was the relic itself which ended up consuming them.