In late 21XX, the Maverick Wars continue with no end in sight. To escape the carnage, humans have begun migrating to the Moon as part of an initiative known as the "Jakob Project", which involves an orbital elevator built in the Galapagos Islands. One night while X is out on patrol, one of the elevators breaks off and comes crashing down to Earth. As X approaches the elevator, the doors open, revealing an entire army of Sigmas. Suddenly, a purple-haired Reploid arrives and introduces himself as Lumine, the director of the Jakob Project. He reveals the "Sigma army" isn't what it appears to be; instead, they are new generation Reploids created as part of the project who are immune from viruses and able to use DNA copy data to change their shapes and appearances to assist with space development.