When Hardison is overriding the network while Monica Hunter is talking on air about poison in the water, he says "Do not adjust your set. I control the horizontal; I control the vertical". This is a reference to the intro to the TV show The Outer Limits (1963).
The "antidote" trimethylxanthine is the chemical name for caffeine. 1, 3, 7-trimethylxanthine to be exact.
The armored vehicle program referenced by the general "XJ12" is the same model number as the Jaguar XJ12, one of the world's first widely available armored passenger vehicle.
The episode title is an obvious riff on the 1975 political thriller "Three Days of the Condor".
This is the fourth time Timothy Hutton has worn an army uniform. The first was Taps (1981), the second was The General's Daughter (1999), and the third in A Nero Wolfe Mystery (2001).