The episodes collected in the release form the middle of the series' mythology, and are centered on alien colonization efforts, the fall of the Syndicate, and Fox Mulder's (David Duchovny) abduction.

The episodes follow the investigations of paranormal-related cases, or X-Files, by FBI Special Agents Fox Mulder and Dana Scully (Gillian Anderson).

The show centers on FBI special agents Fox Mulder (David Duchovny) and Dana Scully (Gillian Anderson) who work on cases linked to the paranormal, called X-Files.

[1][2] Eventually, Mulder has Scully put under hypnosis to learn the truth about her abduction after Cassandra goes missing and her son, Jeffrey Spender (Chris Owens), angrily attempts to push his way up in the FBI.

[3][4] Later, the assassination of a chess grandmaster leads Mulder and Scully into an investigation that they soon discover strikes at the heart of the X-Files; they learn that the real target was a telepathic boy named Gibson Praise (Jeff Gulka).

The culprit is revealed to be Alex Krycek (Nicholas Lea), a rogue FBI agent who formerly worked for the Syndicate, who continues to control the potentially debilitating nanotechnology in Skinner's system in order to achieve his goals.

Hoping to find a cure for her partner, Scully rushes to Africa and discovers a massive wreck of a large spacecraft partially buried in the ocean.

Together, Mulder and Scully locate evidence that proves that Samantha was abducted by The Smoking Man, and was forced to live in a now-abandoned US Army base.

[25][26] Scully soon meets Special Agent John Doggett (Robert Patrick), the leader of an FBI taskforce organized to conduct a search for Fox Mulder.

"[30] The "Biogenesis"/"The Sixth Extinction"/"Amor Fati" trio of episodes started a new mythology for the series, questioning the origin of human life.

Series creator Chris Carter claimed to be interested in the subject for a while, citing the possibility of extraterrestrial involvement in great extinctions that had happened millions of years ago.

Executive producer Frank Spotnitz later explained, "There was a pretty strong sentiment inside and outside the show that it was time to call it a day.

"[34] Eventually, it was decided that Mulder would be abducted at the end of the seventh season, leaving things open for the actor's return in 11 episodes the following year.

Monica S. Kuebler from Exclaim magazine noted that, while the set was "only for diehards, completists", the compilation was "the strongest of the mythology boxes thus far [released]".

He commented on the conclusion of many of the show's long-running arcs, and noted that Mulder was often only a witness to these events, such as the destruction of the Syndicate and the death of his sister.