The episodes collected in the release form the end of the series' mythology, and are centered on those that involve the alien "Super Soldiers" and Dana Scully's (Gillian Anderson) son, William.

Adam Baldwin, Chris Owens, Nicholas Lea, Laurie Holden, and William B. Davis all play supporting roles in the collection.

When Dana Scully (Gillian Anderson) learns that several women have reportedly been abducted and impregnated with alien babies, she begins to question her own pregnancy.

[1][2] John Doggett (Robert Patrick) introduces Scully to Monica Reyes (Annabeth Gish), an FBI specialist in ritualistic crime, shortly before Fox Mulder's (David Duchovny) deceased body suddenly appears in a forest at night.

[3][4] Following Mulder's funeral, Assistant Director Walter Skinner (Mitch Pileggi) is threatened by Alex Krycek (Nicholas Lea) that he must kill Scully's baby before it is born.

Billy Miles, a multiple abductee who disappeared on the same night as Mulder, is returned deceased but his dead body is resurrected and restored to full health.

[9][10] When Miles arrives at the FBI Headquarters, Mulder, Doggett, Skinner and Krycek help Scully to escape along with Reyes who drives her to a remote farm.

Doggett, Scully, and Reyes discover a conspiracy to place Chloramine in the nation's water, causing mutations and creating "Super Soldiers".

[22][23] Mulder returns from hiding to only be discovered looking for classified information at an army base and, after allegedly killing an apparently indestructible "Super Soldier" Knowle Rohrer (Adam Baldwin), he is placed on trial to defend the X-Files and himself.

But with the help of Kersh, Scully, Reyes, Doggett, Spender, Marita Covarrubias (Laurie Holden) and Gibson Praise (Jeff Gulka), Mulder breaks out.

"[36] Spotnitz explained, "What was kind of nice that Chris made the announcement in January is that we had times to wrap our minds around the end and plan for it and give all of the characters their due.

[38] Furthermore, she wrote that the main issue with the release was that "the hardcore fans [of the series] had come to see The X-Files as Mulder and Scully and understandably weren't quick to swallow a couple of new characters running the department.

"[38] Ultimately, she concluded that the poor episodes and the lack of bonus features included with the collection were proof that "Fox seems eager to wash their hands of the disappointing demise of the show".

[40] Joyce Millman from The New York Times called the storyline involving Scully's child—which left her "haunted and irritable"—"a sad misuse of the radiant Anderson".

Club was highly critical of the final season and its mythology story, calling them a "clumsy mish-mash of stuff that had once worked and new serialized storylines about so-called 'super soldiers'".