Robert is taken to Elizabeth Sinskey, the director-general of the WHO, and is given an explanation of what is going on: Zobrist, who committed suicide the week before, was a mad scientist and Dante fanatic who engineered a new virus that would rewrite the human genome to cleanse the world of overpopulation by approximately one third. Elizabeth raided Zobrist's safe deposit box, found the cylinder, and flew Robert to Florence to follow the clues. However, Robert stopped calling in after meeting with Marta and Ignazio, and the WHO feared he betrayed them and was working with Zobrist to unleash the plague. The soldiers were the WHO's SWAT team and never meant to kill Robert.
Zobrist had paid a shadowy consulting group called The Consortium to protect the cylinder until a certain date. When Elizabeth took it away, they were obligated to protect whatever the bone cylinder pointed to. They kidnapped Robert after the meeting with Marta and Ignazio, but Robert hadn't yet solved the whole riddle. They gave Robert drugs to erase his short-term memory, created a fake head wound, and staged every event up to this point so that Robert would be motivated to solve it. Sienna, Vayentha, and Jonathan are all actors working for The Consortium; the call to the U.S. consulate was also staged. The leader of The Consortium, having become aware of the bioterrorism plot, has agreed to cooperate with the WHO.
Sienna goes rogue and The Consortium realizes she was a secret supporter and lover of Zobrist. She learned where the plague is being kept after Robert solved the riddle, and resolves to unleash it by herself. Robert, the WHO, and The Consortium team up to stop her by going to the riddle's actual location: Istanbul, where Enrico Dandolo is buried. At the Hagia Sophia, Robert and the others find the plague is in the Cistern, but discover that Sienna is already there. The bag that holds the plague has been broken, infecting all the tourists inside. Sienna runs out of the Cistern screaming, which causes panic among the tourists who stampede out into the city.
It is discovered Sienna didn't puncture the bag; it was water soluble and had dissolved one week previously in the Cistern waters, meaning that the whole world has already been infected. It is also discovered that Sienna was trying to stop the virus herself, but didn't trust the WHO because samples of the virus would certainly find their way into weapons research. The leader of The Consortium tries to escape WHO custody with help from disguised underlings, but is caught later by Turkish police. It is implied that The Consortium will be investigated and ruined. Sienna receives amnesty in exchange for working with the WHO to address the crisis, since she is a medical doctor and transhumanist writer.
The virus employs DNA modification to cause sterility in humans. The virus has no cure, and even with future technology, changing the human genome back would be hazardous. The human race, therefore, has been forced into a new age of self-understanding.
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