Deserter follows Ryan Johnson and his wife Jen during their flight from the Central Valley of California to Toronto, Canada. Johnson deserted the American army after hearing that he was going to be deployed to Iraq, despite assurances that this would not happen. Like many of his contemporaries, Johnson only joined the army because he could not find a job, and he sees the war in Iraq as both illegal and immoral. Desertion means imprisonment, so he decides to flee, realising that there will be no way back. Johnson seeks advice from various helpful organisations that guide him and Jen to Canada. The employees include both Vietnam veterans and young soldiers who have already served in Iraq.
