...A hearing of the Department of Special Research is inquiring into Sydney's personal connection to the Rambaldi notebook...at which moment she is in Brazil, running for her life -- pursued by armed men and snarling dogs. She comes to the edge of a cliff, and leaps, revealing a para-sail, and descending to safety.
Upon her return to the States, she is detained by the DSR. As the paranormal research division of the National Security Agency, they are searching for an explanation for the image of Sydney on page 47 from Rambaldi's notebook. According to Vaughn, the text around the drawing has been partially decoded and is now being referred to as "The Prophecy."
The CIA is reluctant to cooperate with the DSR, though Haladki does everything he can to assist the rival agency. After undergoing a battery of mental tests, Sydney is asked to submit to a physical exam...
...She refuses and walks away defiantly from the team of DSR researchers. Meanwhile, SD-6 has identified "the Man" responsible behind Mr. Sark and McKenas Cole. Using the evidence gathered in Brazil, Sloane identifies Alexander Khasinau, a dangerous and well-connected ally of the Russian mob.
The 12 members of the Alliance, the force behind SD-6 and its eleven sister cells, have called an emergency meeting to discuss the situation.Will they go after Khasinau and his group, or shall they vote for détente -- Sloane desperately hopes that they will vote for war, but he doesn't know where the votes will fall.
Fishing for information, he calls Edward Poole, the leader of SD-9. Poole insists that Alliance member John Briault has been cooperating with Khasinau. Sloane is reluctant to believe that such a trusted, old friend could be cooperating with SD-6's latest enemy... but he finally decides to resolve the situation himself.
In an act of kindness, Sydney meets with Sloane's dying wife Emily, who reveals that her cancer might have been treated had she not denied the truth for so long. With these words as a warning, Sydney submits to further testing by the DSR.
Later, Jack reveals that the DSR agents do not have the original code key to decipher Rambaldi's writings. The original key is held at the Vatican... In a daring gamble, Sydney persuades Vaughn to break into the Vatican with her.
During their adventure, Vaughn flirts and asks her to dinner at his favorite restaurant in Rome. Engraved into the frame of a Rambaldi painting - located in the Vatican's subterranean archive - is the code key. Sydney and Vaughn photograph the cryptic writing, narrowly escaping Vatican guards and never making it to dinner.
Meanwhile, Sloane has discovered that "page 47" of the Rambaldi manuscript is a counterfeit. He's furious and demands to talk to Sydney. Does he suspect her?
Before the Alliance's meeting, Sloane arranges a private rendezvous with John Briault - the traitor Poole accuses of aiding Khasinau. Quietly, and without emotion, Sloane assassinates his friend in a Montreal park at night.
When the Alliance meets, the decision to retaliate loses...by a single vote. Sloane realizes that it was Poole - not Briault - who has been working for the enemy all along and Sloane promises to "return the favor."
At the CIA, Vaughn provides the code key to decipher Rambaldi's writings, which only confirms what the DSR has already discovered...and he is not pleased. Sydney is taken into custody, plucked from a nightclub where she has met up with Francie and Will, and "The Prophecy" is finally revealed to her.
According to Rambaldi, a woman bearing Sydney's characteristics will appear - she will fulfill the prophecy and "render the greatest power unto utter desolation". Sydney is driven away in chains and shackles by the DSR...now a prisoner of a 15th century prophecy...