The X-Files has been shut down and Mulder and Scully are separated. Scully finds herself teaching classes at the FBI Academy in Quantico, Virginia, while Mulder is assigned to surveillance duty. With Agent Alex Krycek as his new partner, and the mysterious X as his new source of information, Mulder struggles to keep his search for the truth alive. But ironically it is Scully who experiences the close encounter Mulder has longed for, taking a journey that will ultimately bring the two agents back together and forging a bond that will make them closer than ever before.

Mulder is missing and assumed dead . . . although Scully experiences a vision in which he is still alive. Yet even as they are reunited, each must deal with an additional personal loss, tragedies that ultimately serve to strengthen their connection to each other. And they soon find themselves depending on that strength as familiar foes resurface and preconceived notions are shattered.

As Mulder lies in a neurological unit, his brain under attack by a deadly onslaught of electrical impulses, Scully struggles to decipher strange symbols covering a spacecraft found submerged off West Africa's Ivory Coast. But the connection between these two phenomena is just the first of many challenges the agents are destined to confront. For they are about to enter a time of closure and a time of new beginnings. For Mulder there's the death of his mother and Diana Fowley, and the end of his search for his abducted sister, Samantha. For Scully it is a time to face her own personal demons, among them the return of death fetishist Donnie Pfaster. Yet just as Scully faces the ultimate new beginning, the ultimate horror occurs — the abduction of Mulder.