A UFO is shot down over Scotland while it was sending a signal into space. Frustrated by the RAF cover-up, the pilot who downed the craft teams up with a scientist who caught its transmission to find out what craft was.

After a yellow portal appears for a short time trying to drag in the UFO pilot, they decide to remove the implant discovered in his teeth. But as the implant is taken for analysis another portal appears which draws Friday, Tucker and three soldiers into it. Frustrated at his inability to stop it, Reece condones a brutal interrogation of the pilot.

While they manage to get some of the UFO's systems working, the pilot finally tells his story.

The town of Kirkhaven becomes the focus as more and more of its inhabitants succumb to the disease spread by Cdr. Friday. Meanwhile Shay tries to find a way to detect the gates, while Preston researches a ND toxin.

A huge black hill appears outside Kirkhaven, slowly enveloping more and more land. When even heavy artillery fire leaves it unharmed, Reece decides that someone must try to fly though it and gather data.