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We have a question that lists which episodes are MOTW and not part of story arcs.

But what it does not cover, when looking at the arcs, is what ARE the main story arcs in X-Files?

Are they mapped 1-1 to seasons or cross season boundaries?

Spoilers: Please assume that the reader knows the high level ideas of X-Files and saw some episodes but doesn't know all the details and therefore appropriately apply spoilers to important reveals that are still needed in the arc description, e.g.

Scully's pregnancy

I NOT interested in specific episode lists, just what the arcs are.

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    Weird stuff. Weird stuff. Aliens. Aliens. ALIENS. Weird stuff. Aliens. Aliens. More aliens. – Omegacron Oct 24 '14 at 20:17
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    "The Truth is Out There". That describes everything. – BBlake Oct 27 '14 at 13:52
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The X-Files had many story arcs, which typically spanned across seasons. You can get a very good idea of what those arcs are by looking at the 4 "X-Files Mythology" DVD sets that were released in 2005. Each DVD set focuses on a few arcs and contains only the key episodes pertaining to those arcs.

The following are descriptions of each DVD set from Wikipedia:

The X-Files Mythology, Volume 1 - Abduction:

The episodes collected in the release form the beginning of the series' mythology, and are centred on alien abduction at the hands of "colonists".

Additional details with spoilers:

Events covered in the episodes include the meeting of Mulder and Scully, the introduction and assassination of a secretive informant, the apparent return of Mulder's lost sister, and the abduction and return of Scully.

The X-Files Mythology, Volume 2 - Black Oil:

The episodes collected in the release form the middle of the series' mythology, and are centered on the discovery of a mind-altering extraterrestrial "black oil".

Additional details with spoilers:

Events covered in the episodes include the assassination of a secretive informant, Scully's diagnosis with cancer and Mulder's apparent suicide.

The X-Files Mythology, Volume 3 - Colonization:

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, [spoiler removed and placed in next section]

Additional details with spoilers:

and Fox Mulder's (David Duchovny) abduction. [...] Events covered in the episodes include the discovery of alien-human hybrid Cassandra Spender (Veronica Cartwright), the destruction of the Syndicate; the discovery of the remains of a space ship in Africa; the fate of Mulder's sister, Samantha; and the abduction of the former, as well as the subsequent hunt for him under the direction of John Doggett (Robert Patrick).

The X-Files Mythology, Volume 4 - Super Soldiers:

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.

Additional details with spoilers:

Events covered in the episodes include: the return, death, and resurrection of Mulder; the birth of Scully's child, William; the discovery of the "Super Soldier" conspiracy; the discovery of the remains of a space ship in Canada; Scully's choice to give William up for adoption; and Mulder's trial, conviction, escape, and discovery of the truth.

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Cross-season arcs include Mulder's search for his abducted sister, Scully's abduction and cancer, black oil, military "Super Soldiers," etc. Most if not all of the overarching story arcs are alien-related.

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    "etc..." does not help much – DVK-on-Ahch-To Oct 28 '14 at 21:53
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The answer of @pacoverflow above is, of course, correct. That being said, if you want an answer with minimal spoiler potential and which is still technically correct, I would say there are only really two main story arcs: original syndicate (seasons 1 to 7) and new syndicate (seasons 8 and 9).

Season 7 is, in some sense, a very long epilogue to the original syndicate story arc.

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