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Most wanted terrorist Saif Rahman Yasin, known as the Emir, secretly enters the United States by private plane. Having altered his physical appearance and living in the state of Nevada, he coordinates his massive operation as leader of terrorist organization Umayyad Revolutionary Council (URC), codenamed Lotus. It aims to weaken the current presidential administration with a series of seemingly isolated terrorist attacks and culminating in the destruction of the Yucca Mountain nuclear waste repository, using a nuclear device assembled from radioactive material stolen from an abandoned nuclear waste storage site in Russia, in order to poison the water table for the western United States.
After successfully foiling a hostage situation in the Swedish embassy in Tripoli, John Clark and Domingo Chavez are forcibly retired from their duties in the CIA and Rainbow. They are then recruited into The Campus, where they take part in the organization's hunt for the Emir, which spans through Sweden, Pakistan, Canada, and Libya. They suffer a tragedy when operative Brian Caruso died due to injuries sustained during a firefight with his brother Dominic against URC terrorists in Tripoli. After further investigation and at one point cooperating with National Counterterrorism Center deputy head and Clark's longtime friend Mary Pat Foley, The Campus later deduce that the Emir is in the U.S.
Meanwhile, former president Jack Ryan is working on his memoirs and initially refusing to speak out against his successor, Ed Kealty. When he finds out that the Kealty administration are planning to prosecute U.S. Army Ranger Sam Driscoll for murdering sleeping Middle Eastern terrorists in a cave during their fruitless search for the Emir, he decides to announce his candidacy for President of the United States in the next election. After the announcement, charges against Driscoll are dropped and he was given an honorable discharge. Clark later recruits him into The Campus. Additionally, Ryan finds out that his son Jack Ryan, Jr. is working for The Campus as an analyst, which he reluctantly accepts.
URC terrorists destroy a Petrobras oil refinery outside São Paulo, Brazil and trigger a series of attacks on small towns across the United States. Jack and Clark later thwart the destruction of a cargo ship carrying flammable material, killing the Indonesian perpetrators tasked by the URC. Chavez and Dominic are sent to Brazil in order to investigate the refinery incident and later capture a URC courier, who reveals that the Emir is in the U.S. and coordinating the attacks. Along with Clark and Jack, they proceed to Las Vegas to apprehend him, preventing him from blowing up the Yucca nuclear waste storage facility in the process. After returning to Virginia, they interrogate him by injecting him with succinylcholine and simulating a heart attack, allowing him to confess his crimes and reveal the plans behind Lotus, which involves the cooperation of Pakistani intelligence in conquering the country and securing their nuclear inventory (to be continued in the next novel Locked On). After a day of interrogations, the Emir was covertly given by The Campus to the FBI in order to be imprisoned and charged by due process of law.
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