"I am not a criminal," Flynn said in a jailhouse interview.
The 37-year-old mom was arrested over the weekend on desertion charges, 10 years after leaving her military post.
"I love my country, I love my honor to country, to serve, but that's not the point," Flynn said.
Flynn said that in 1999, her then 4-year-old son, Vidal, and 8-year-old daughter, Jackie, had been staying in San Diego with a close friend while Flynn was in basic training at Fort Gordon, in Georgia. During that time, her son got extremely sick.
"My son had pneumonia, he wasn't talking any more, he had ringworm," Flynn said.
Flynn got a 10-day emergency leave from the military to come back and take care of her son. After that experience, she didn't want to leave her kids with friends and she didn't have any family who would take them. She also said the Army wouldn't let her bring her kids to Fort Gordon because trainees were not allowed to have children on base.
"If someone told you to turn your children over to Child Protective Services instead of trying to find you a better solution, you wouldn't do it either," Flynn said. "You would have done the exact same thing."
A few months after deserting the Army, Flynn said, she twice tried to turn herself in at local Navy installations but was told to go home.
"Because of the kids," Flynn she said.
Ten years later, she is waiting for the military police to pick her up at the Las Colinas Detention Facility.
"I am scared to death," Flynn said. "I don't know what's going to happen."
A military lawyer said the Defense Department could decide to separate her from the Army without any punishment.
"Her case could also be tried as a court-martial offense," former Judge Advocate General Mike McCloskey said.
If convicted, Flynn could spend years in military prison, McCloskey.