Thomas Fleckenstein, the state's attorney in Anne Arundel County, Maryland, said the facts show that the boys' grandmother was co-conspirator of an international kidnapping weeks in the making.
"She participated in the planning of the removal of the children from Maryland," Fleckenstein said. "She participated in the story that was told to the father as to where the children would be in New York, when they would be back. The fact that she was visiting was part of the impetus for the father allowing the children to visit and spend time with the grandmother. And she was actively involved in the helping the children travel to Egypt."
Shannon turned to an Egyptian court for help, hiring an Egyptian attorney to help him enforce his U.S. custody rights. The case was filed in 2002 but postponed until 2004. It was then postponed another two years, and nothing has happened since.
Officials from the U.S. State Department told him there was nothing they could do.
"The State Department won't get (photos) because they said the family won't allow it, it's intrusive," Shannon said. "I've asked for welfare-wellness (visits), and the embassy writes letters to the family and the family simply refuses them."
There might have also been another reason for the State Department's lack of interest.
The boys' grandfather, Osama Khalifa, was a successful businessman in Egypt who sat on several government boards of then-President Hosni Mubarak. In late 2001 and 2002, in the aftermath of 9/11, the United States was leaning heavily on Egypt and Mubarak for support in the war on terror. It might have been a bad time to bring up the kidnapping of two boys by a family with ties to Mubarak.
Shannon felt very alone. He received a letter from his ex-wife's sister, Eman, who wrote that the children need to be with their mother because of Islamic law. She also told him to give up --"force and bad tactics will only serve to put you farthest away from your objective."
The other side of the story
Nermeen Khalifa now lives in Heliopolis, an upscale Cairo neighborhood where her father runs his consulting business.
For years, she has kept her silence, only once agreeing to an interview with an Arab media outlet. But she agreed to talk by phone to CNN.
She has a completely different account of her marriage to Shannon, the boys' kidnapping and the U.S. court record on the case.
For example, Shannon says his ex-wife had a drinking problem. Maryland police records show she was charged with assaulting her husband and placed on probation, ordered to undergo treatment at an alcohol and drug rehabilitation center.
But Khalifa says it was Shannon who was the alcoholic and that it was he who kept the family apart. She also puts blame on the American judicial system, which she says is biased and discriminatory against Arab Muslims.
"I left with my kids on my accord to protect myself and my sons," she said. "(Shannon) is a manipulator, he's a liar, and I had to leave. The system was against me."
On September 11, 2001, the very morning that terrorist planes were hitting the World Trade Towers, a Maryland state court issued a warrant for Nermeen Khalifa's arrest and granted sole custody of her sons to Shannon.
To her, the date of the hearing -- and her absence from the court -- proves she is a victim of discrimination.
"The ruling happened on 9/11. So what more do you want?" she said. "The judge ruled custody without even hearing me or seeing me or knowing anything about me. He gave (Shannon) immediately custody of both kids."
Khalifa says she is "tired of this saga" and that Shannon has been making her life miserable.
"If he's so torn up over the boys, why hasn't he once tried to send them a birthday card, a Christmas card, anything, let alone come here so that he can see them?" she said.