A Swipe is a chip which was inserted by WICKED into each subject's brain before the Trials began. It wipes their memory and allows WICKED control over the subject's actions. Examples of this are Gally throwing a knife at Thomas, Chuck jumping in the way of the knife (both in The Maze Runner) and Teresa's difficulty to speak and hug him in the shack when she meets Thomas again in The Scorch Trials. They also provide Thomas, Teresa, Aris and presumably Rachel access to WICKED's telepathy network, which allows them to communicate telepathically.
At the start of The Death Cure, WICKED offer to remove the subjects' Swipes. Thomas, Newt and Minho are the only three subjects who don't allow WICKED to remove their swipes, partly afraid of the past and partly afraid of what WICKED would do to their brains. Eventually they realise that they need to have them removed so WICKED can no longer control their actions, so Jorge and Brenda take them to see Hans, an ex-WICKED scientist. When he goes to set up his machine, however, WICKED's control over Thomas kicks in, and after a brief struggle with the control because they aren't close enough for full control, he picks up a knife and attempts to kill Hans. It takes the other four to finally get him on the bed and drugged so they can remove the Swipe.