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The Trace was a piece of computer software that the CIA had picked up from the DIA during Miracle Day. It detected the "vine technology" that, according to Noah Vickers, the Three Families used to "piggyback their calls on 50,000 different lines", and found its source. The CIA used it to find the double agent employed by the Families.
Although Noah, who used the program to find the mole, was bombed along with his newly found information, he managed to get the program's findings transmitted to Rex Matheson, who had her shot. (TV: The Blood Line)