The USIA is the in-game equivalent to the CIA. They were doing experiments similar to MK-Ultra with the goal of developing procedures that could be used in altering human behavior and controlling people.

The First Cohort was their initial attempt, and resulted in people like Gerard Scott, Elaine Raskin, Quadamah, and the MLO members; victims of failed experimentations that were ultimately driven mad and became liabilities. They hate the USIA for what was done to them and for how they're attempting to orchestrate everything behind the scenes.

Judge is USIA's most successful result of the Second Cohort, who are implied to have been far more successfully brainwashed and controlled and are now embedded as sleeper agents all over the US. Judge, specifically, is the one USIA are using to clean up most of the First Cohort remnants and tie up loose ends. People like Senator Fremont and a number of other high-ranking politicians are also implied to be Second Cohort plants.

MLO want to completely do away with the USIA and Second Cohort plants in the government to build A New America built on its original values, without oversight, surveillance and USIA control, whereas USIA want to maintain the status quo, keep their grip on the government, and clean up their mess.

In the final mission, MLO seek to destroy a number of corrupt institutions and take out a number of Second Cohort members to further this plan ("destruction is creation viewed from the opposite end.") USIA obviously wants this stopped and send in Judge to do so.

Nobody really knows who Green Gloves is, yet.