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From the article:
The finder at one point attempted to restore the phone by connecting it to a roommate’s Apple computer, but was unsuccessful.

THAT is how Apple and the police tracked this thief down. I'm sure Apple was on the lookout for the prototype iPhone's device ID via iTunes. The minute this guy connected to a Mac, the iTunes account associated with that Mac told Apple everything they needed to know about the location of the iPhone.

Mark
 
The article goes on to verify that the thief "shopped" the iPhone around to various news sources, looking for money in exchange for the "exclusive". Note at the bottom of the article that Wired was contacted and declined when the person made mention of requesting payment.

Mark
 
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