'Double Blind' by Matthew Teague, the untold story of how british intelligence infiltrated and undermined the IRA during the Dirty War.
'The Coming Normalcy?' by Robert Kaplan, a profile of 1/25, a stryker brigade in Mosul, describes how the soldiers themselves are planning ops, often by passing the TOC entirely.

The author also mentioned an interview with an Algerian officer who when asked how they defeated their own islamic insurgency in the 1990's replied that it was quite simple--the army quietly killed a large number of people with no journalists around. If it were only that easy in Iraq.

Although considered a liberal magazine, I find the Atlantic has some of the best journalism around.