The 7-year-old twins were reported missing after their mother, Susan Boggs, said she dropped them off Halloween Sunday to visit their father, but they were never returned.
Boggs said she was concerned because both of the siblings had breathing conditions that required medicine their father didn't have.
The kids were last seen nine days ago with their father by clerks at Roses in Cary's South Hills Mall.
"So many days of not knowing where they were what was happening to them what was going on," Boggs said. "He lied to them and wouldn't let them call me, just he had them thinking some bad things."
Police said they tracked the children and Alvin Allen through several states.
"We came by some information that said he was located in West Virginia and that we had just missed him at a motel in West Virginia and that information we received showed him going south possibly to Jacksonville, Florida," Erwin Police Chief Warren Morrisette said.
On Tuesday, Highway Patrol officers caught up with Alvin Allen in McIntosh County - south of Savannah, Georgia with the twins in his car with him.
A short time later, Boggs received a phone call that Alvin Allen had been pulled over and her children were fine. She headed from Erwin to Georgia just minutes after she spoke with Alyssa and Alex.
She told ABC11 Tuesday that she believed Alvin Allen took her children to avoid having to pay child support. He was scheduled to appear in court next week, because of unpaid child support.
After authorities located Alvin Allen, he was placed in jail, while the children were put in foster care until their mother arrived.
Boggs was reunited with her children Wednesday morning. They returned home around 6 p.m.
The Erwin police chief and officers were the first people Boggs publically thanked for helping bring the ordeal to a happy ending.
Boggs' mother, Judy Boggs, said Wednesday night was what she had prayed for --hugging and kissing her two grandchildren.
"It was a terrible week, I've never felt like this before," she said. "It was extremely hard, but today has been the most beautiful day in the world they are just gorgeous."
Police say Allen remains in jail in Georgia on misdemeanor charges of keeping the children out of school and not taking care of their medical needs.
They say Alvin Allen has waived extradition and should be returned to North Carolina within the next week.
Boggs says she is going to court to get official custody of her children.