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2a. it contains a list of all references (sources of information), presented in accordance with the layout style guideline.
2b. reliable sources are cited inline. All content that could reasonably be challenged, except for plot summaries and that which summarizes cited content elsewhere in the article, must be cited no later than the end of the paragraph (or line if the content is not in prose).
If you are going to make comments on things that happen during the plot in later sections, at least have them in the plot section as well. I.e. Kristen shaving Mulder.
Plot section does not need to be referenced. Also, it is overly long for an article of this length (nearly half the article).
1A
Lead
Too many simple sentences; "it was... it was..." etc.
"negative reviews from both critics and the show's crew" --> "reviews from both critics and the show's cast and crew" (Duchovy didn't like it either, right?)
Plot
Who is John? He "comes back" from where? Is he the true Son?
Apparently, yes. (the blood bank receptionist calls him "Frank", but Kristen says his name was "John" before becoming The Son, which is the preferred name to prevent confusion)
Make sure points which you discuss later on are mentioned in the plot.
Broadcast and reception
The quote from Nutter is overly long. It should be paraphrased and worked into another paragraph for now.
He is a published critic, and regarding reviews are reviews, done by the editorial staff and don't violate the WP:RS parts that state "with the exception of material on such sites that is labeled as originating from credentialed members of the sites' editorial staff, rather than users".
After each sentence with a direct quote you should have a reference.
What is Starpulse, and why is it reliable?
Reference formatting needs to be standardized. You have linked and non-linked harv references; you should only have one style
Removed and fixed.
3A
Assuming you have the Season 2 DVD, you should be able to get further information on the production from the commentary / making of feature. Also, what about major newspapers like the New York Times? Many of them have good archives that you can browse for reviews, or type a string like " site:nytimes.com 3 X-Files " into Google.
Added paragraph on filming to Production.
6A
We have a picture of Duchovny and whatnot that could be used to illustrate him further down the article.