WMG / Covert Affairs

Henry Wilcox is known to run black ops - he's the freakin' Prince of Darkness, for crying out loud. He's the only person who could avoid Arthur's polygraph test, because he's technically not part of the agency. His son, Jai, knows Ben. He's framed Ben for the leak, so Joan and Arthur are hunting him down. Ben thinks Joan and Arthur have betrayed him. Really, he's pitting them against each other as part of his master plan.
  • Confirmed in the first season finale, when Liza Hearns gets into a car with him and he makes a comment about "getting her to win that Pulitzer Prize."

Ben's mission in Sri Lanka was connected to Auggie's mission in Iraq.

They both happened around the same time, and were both dark ops. Perhaps Ben's screw-up in Sri Lanka led to Auggie's IED?

Giving Annie's new boss the name Lena was intentional given Piper's past filmography with another Lena.

Henry Wilcox has finally let Annie in on the truth about Ben Mercer.
We know as of Season 1 that Arthur and Joan Campbell agreed to bring Annie into her position to help see if Ben could be located. Given the heavy implication in-universe to Annie that she was brought in off the Farm early because the DPD saw potential in her, finding out that she was nothing more than bait for Ben would have to hit pretty hard.
  • Jossed

Henry Wilcox wanted Annie to tail him.
He tosses off a seemingly random comment: "When I was at the farm, they taught us to use our mirrors." Now, he was ostensibly criticizing Annie's driving, but it does have another meaning. As a very experienced spy, he'd know when he's being tailed. And one common trick to check if you're being tailed is to look in any reflective surface and see who might be a little too interested in your movements from point A to B.

The Big Bad of the Fifth Season is the head of Mc Quaid Security.
He probably has some kind of hidden agenda or bone to pick with the CIA and is determined to effectively supplant the CIA as a whole by becoming their premier contractor when the DCS decides in-house personnel are unable to effectively secure their black sites.