The Immunes, commonly known as "Munies", are the very small percentage of the remaining population of the world that are immune to The Flare. It is revealed in The Death Cure that less than 1 percent of the remaining population have immunity to it. The majority of the Gladers are Immunes.
"Munies" are generally hated among the rest of the population, due to envy. They have been described as valuable, and many are captured by bounty hunters and sold to WICKED. The Right Arm was against this treatment of the Immunes, and kidnapped a bunch of them, among which included Thomas, Brenda, Jorge, Minho, Aris, and Teresa. They attempted to trick WICKED into allowing these Immunes into the headquarters, a plan which failed.
After Thomas rescued the Immunes holed up in the Maze, they went through Chancellor Paige's Flat Trans, and arrived at a paradise, where they are meant to live and repopulate the Earth, while the Flare-infested section dies off.