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 offers 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 realize that they need to have the Swipes 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. After Thomas has a brief struggle with WICKED over the control of his brain (because WICKED isn'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 Hans can remove the Swipe.