The Question and Answer section for The Death Cure is a great resource to ask questions, find answers, and discuss the novel.
A few things happen to Newt. What chapter are you referring to?
The Swipe is a micro-chip that e is inserted into the brain to wipe out the participants memory before they participate in the Trials.
The note meant that Newt trusted Thomas only, and somehow he knew that Thomas will be the only one to fulfill Newt's wish, which is to die.