The Department of Special Research is inquiring into Sydney's connection to the Rambaldi notebook. As the paranormal research division of the National Security Agency, they are searching for an explanation for the image. According to Vaughn, the partially decoded text around the drawing is 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. Sydney refuses to submit to a physical exam. Meanwhile, SD-6 has identified "the Man" responsible behind Mr. Sark and McKenas Cole -- 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. Sloane 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 it, but decides to resolve the situation himself.
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. Sydney persuades Vaughn to break into the Vatican with her.
During their adventure, Vaughn asks her to dinner. 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.
Before the Alliance's meeting, Sloane arranges a private rendezvous with John Briault. Quietly, and without emotion, Sloane assassinates his friend in a Montreal park at night.
The decision to retaliate loses by one vote and Sloane realizes that it was Poole, not Briault, who has been working for the enemy.
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.
Vaughn: You're being investigated by the DSR.
Vaughn: Department of Special Research. And it was created during World War II to investigate Nazi interest in the occult. After the war, an executive order was signed, empowering them to investigate fringe science, uh, parapsychology, remote viewing--
Sydney: What do they want with me?
Vaughn: They want to know why your picture is in the Rambaldi book. No, I know it seems ridiculous.
Sydney: This drawing is five hundred years old. Millions of women have looked like that. My mom looked like that. Maybe it's a picture of my mother.
Sloane: Using all available resources, we have finally tracked down the enemy who we no longer have to refer to as The Man. Thanks to the surveillance photos you obtained in Brazil, we have confirmed his identity. He is Alexander Khasinau.
Emily: For four months, I did nothing. I was so terrified of what I did not know. I was so terrified that I was paralyzed. And the longer that went on, the more terrified I got. Wanting to know the truth but being too afraid to find the answers.
Sydney: We'd have to leave tonight. You in?
Vaughn: (shy smile) Yeah. I'll break into the Vatican with you.
Sloane: Our conversations were never recorded. We talked on secure lines. I made sure I met Briault in secret. You used me.
Poole: I haven't the slightest idea what you're talking about.
Sloane: I will repay the favor.
(As the FBI is taking Sydney into custody.)
Vaughn: Those medical tests you took, they were looking to match three specific anomalies Rambaldi mentioned: DNA sequencing, platelet levels, and the size of your heart. You match all three.
Sydney: So what does the prophecy say?
Evans: "This woman here depicted will possess unseen marks. Signs that she will be the one to bring forth my works. Bind them with fury, a burning anger unless prevented at vulgar cost this woman will render the greatest power unto utter desolation."