Allegiance takes place in October 2004 and concerns the upcoming deployment of a New York Army National Guard unit to Iraq.

First Lieutenant Danny Selfton, the executive officer of his company, was transferred to a non-deploying public affairs unit due to influence from his politically powerful father but is present to assist in the final preparations.

Specialist Reyes, a combat medic in the same unit, applied for a compassionate reassignment due to his son suffering from lung cancer.

However, his request for reassignment was denied by his battalion commander Lieutenant Colonel Owens due to his needed medical skills for the upcoming deployment.

Shortly after they flee Selfton is caught and arrested by the military police on base while trying to contact Reyes' cousin on a pay phone.