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.
While the Flare has a high mortality rate among the non-infected, the small percentage of humans have produce special enzymes from their immune systems that can gradually neutralize the virus overtime and give immunity to the side effects of the Flare. It was because of these special enzymes that give WICKED the idea of creating the Maze Trials. If an immune individual is in a constant state of stress, the human body reacts quickly to produces the enzymes that are found in the brain cells that can sterilize the virus and break them to pieces. However, Immunes can infect non-Immunes through interaction between the two as Immunes have the virus yet it does not affect them.
Most of the enzymes can only be found in humans under the age of twenty because the youngest tends to have higher metabolism and immune system.
In The Death Cure, many Immunes were 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, Teresa, Minho, Aris, Brenda, Jorge. 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-infected population dies off.