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For example:

"The fact of the matter is[,] we have a government that will do what it wants to do for the next two years."

"The fact of the matter is[,] he lost because he didn’t try very hard."

"I'm no scientist, but the fact of the matter is[,] I've lost ten pounds in two weeks on my shake diet."

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With or without "that" you do not use a comma in any of your sentences after The/the fact of the matter is.

"The fact of the matter is[,] we have a government that will do what it wants to do for the next two years."

You have a Complex Sentence here with a main (independent) clause and several subordinate (dependent) clauses:

The fact / of the matter / is / (that) we have a government / that will do / what it wants to do for the next two years

The subject in this sentence is "fact" and the verb is "is." You do not put a comma after the subject of a sentence. The noun clause coming after "is" has the relative pronoun (that) which is omitted because it is understood. The relative pronoun is often omitted in a noun clause.

CORRECT: "The fact of the matter is we have a government that will do what it wants to do for the next two years."

CORRECT: "The fact of the matter is that he lost because he didn’t try very hard." [include that for clarity]

CORRECT: "I'm no scientist, but the fact of the matter is I've lost ten pounds in two weeks on my shake diet." [Compound-Complex Sentence]

I am no scientist / but / the fact of the matter is / (that) I have lost ten pounds in two weeks on my shake diet

Main independent clause / coordinating conjunction / independent clause / noun dependent clause

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    Since English barely has any set punctuation rules and you don't cite even one, this seems highly subjective. – Helmar Aug 29 '16 at 9:19

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