In the final moments of a cooperative mission, Sydney and her Russian nemesis Anna memorize a 500-year-old binary code written by Milo Rambaldi before it is destroyed. Sydney's inner conflict -- as to whether she should give the correct sequence to SD-6 -- is confronted by Agent Vaughn, who makes it clear, in no uncertain terms, that her role as a double-agent is in constant jeopardy.
The completed code represents a geographical location for a church in Málaga, Spain, where Sydney and Anna once again meet up – this time as opponents. Sydney bests Anna in a brutal fight, and recovers a gold circular crystal from the church's stain glass window.
She returns it to SD-6, where Marshall's analysis discloses a pre-synthetic polymer, also invented by Rambaldi...The 15th century seer's progressive inventions now appear to be at the root of a much deeper mystery...
Sydney and Dixon are sent off on their next mission – to investigate a plot to eliminate the United Commerce Organization. In Casablanca, Morocco, Sydney adopts the guise of a French-Canadian tourist.
In a crowded marketplace, she attempts to get near Luc Jacqnoud, whose bodyguard recognizes her from a previous encounter in Corsica. After a powerful battle, Sydney arrives to Dixon's aide, and is crushed to find that their contact, Bak Ibrahim, has only just been slain...a friend, whose life she could not save.
At SD-6, Jack is interrogated by McCullough – but we reveal, in a dreamlike sequence, that a unspoken truth about Sydney's mother continues to haunt him. Meanwhile, Vaughn's feelings for Sydney, in a moment of briefing, show through even further – finally, when she breaks down to him about the heartbreaking conflicts in the career of a dual agent, Vaughn offers her his support as a friend.
Meanwhile, Francie's suspicions grow of Charlie's infidelity, so she and Sydney stake him out, CIA-style, until they spy him kissing another girl. And Will unravels further clues about Danny's death and struggles with his own feelings for Sydney.
SD-6's latest clues lead Sydney and Dixon to São Paolo, the location of the next United Commerce Organization conference, where Sydney witnesses the method to Jacqnoud's scheme. Dhiren Patel, the Peace Prize winner, is scheduled to speak at the UCO conference, but collapses at an evening social, before being rushed away by men impersonating a paramedic team...to a nearby refinery, instead of a hospital. And while Sydney observes from the rooftop, a tiny bomb with a charge equivalent to 300 pounds of TNT, is surgically implanted into Patel's pacemaker...