After several failed attempts to attain conscientious objector status, he deserted his unit in Germany in September 2006 to avoid redeployment to Iraq.

Before a deployment, he applied for retroactive conscientious objector status in February 2004, but was denied,[3] reportedly by a vote of two to one by the three-person panel.

When military police came to his home in Schweinfurt, Germany on September 2, 2006, he climbed out of the bathroom window, going AWOL for 24 days.

"[4] An army prosecutor dismissed Aguyao's reasoning, stating, "His service was going to be important as a medic regardless of whether he was carrying a weapon or not.

[7] Following his conviction, Amnesty International named Aguayo a prisoner of conscience, arguing that he had taken "reasonable steps to secure release from the army" and that he was "imprisoned solely for his conscientious objection to participating in war".

[2] Aguayo began a speaking campaign at U.S. schools to bring awareness to young people and educate them about the realities of war.