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.
Back in the United States, CNN got a phone call from a young man who said he was Adam. He asked that most of the call be off the record, but he did allow CNN to record a quote about his mother: "She's a great caring mother, very considerate and she does whatever I ask her. If I asked her this moment to take me to the United States and give a ticket, she would proudly do it without hesitation."
Shannon believes his ex-wife has turned his sons against him. But against all odds, he still remains optimistic that his sons will turn 18 and leave Egypt on their own, learning the truth about their father: that he never stopped loving them and that he never stopped trying to be their dad.
"It's like they say in Egypt, 'Inshallah,' (If) it is God's will," he said. "They have to come back to the United States. They are U.S. citizens."