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.
Shannon says he has tried to talk to his boys every year, but the Khalifa family has refused to put them on the phone. He has also sent e-mails to them, but they go unanswered.
Six years ago, Shannon said, he was allowed to talk to Adam on the phone on his 10th birthday. But it wasn't the boy he remembered.
"He was, 'I hope bulldozers knock your house down and they burn your house,' " Shannon said. "He's been watching too much of the Israeli/Palestinian thing."
When asked why she hasn't sent a photo to Shannon or even posted one online, Khalifa says no one has asked.
"I'm not keeping (the boys) from their father," she said. "He can come here anytime and meet them."
First look in a decade?
Last month, in an undercover van, CNN went to the apartment where Khalifa lives with her two sons. It was Sunday morning, the beginning of the school week in Egypt, and two young men walked out of the building and into a private school bus.
When he was shown this on video, Shannon became emotional. He didn't recognize his sons.
"If these are my sons, it's the first time I've seen them in 11 years," he said.
Khalifa said in an e-mail that the boys in the video were not her sons, and then in a phone call, she threatened to sue CNN if the images were broadcast. When asked why she would consider a lawsuit if the photos were not of her sons, she didn't answer.