This episode begins three years in the future with Captain Archer and Degra (the mastermind behind the Xindi weapon project) aboard a shuttle escaping from a Xindi Insectoid prison camp. Degra cannot remember being a prisoner, but Archer convinces him that this is due to the blood worms in his system (used by their captors because they excrete a truth drug). He removes a worm from Degra's arm.
It unfolds that they are in fact in a simulator inside Enterprise (and not 3 years in the future) and the whole set up is a ploy to find out from Degra where the weapon is being constructed. The worm in Degra's arm was inserted by Dr. Phlox. This is partially successful, and Degra inputs some coordinates into the navigation system, but then becomes suspicious during a malfunction in which one of the windows of the simulator shows itself to be a screen by reverting momentarily to static.
This leaves the crew with a problem; investigating the coordinates would take them 3 weeks, time they do not have to waste on a wild goose chase. Instead they again deceive Degra into thinking that they have utilized some of the Xindi technology to travel faster, and trick him into thinking that they have already arrived at the coordinates. Degra shouts in defiance that they will never be able to get through the perimeter guards and destroy the weapon, thus proving that the coordinates do in fact relate to the weapon. The episode ends with the ship heading for the weapon coordinates.