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In Bosnia and Herzegovina, Al Qaeda in the Balkans leader Tarik Brkić, who is of Chechen descent, is tasked by his mysterious benefactor Red Wing to orchestrate false flag attacks on Croats, Bosniaks and Serbs in order to disrupt the Unity Referendum, an upcoming national gathering which aims to promote equality among the three rival ethnic groups. At the same time and without Red Wing's knowledge, Brkić also plans to provoke the Russians, who happen to be staging a military exercise nearby, into military action in the Balkans by arranging a terrorist attack, which would then incite NATO to intervene, resulting in a new world war. He obtains eighty thermobaric warheads as well as the accompanying missile guidance system, stolen from a Russian armory in Syria and smuggled into the country, for this purpose.
Meanwhile, Jack Ryan Jr. goes on an accounting job as a financial analyst for Hendley Associates in Ljubljana, Slovenia, on behalf of a Slovenian company which is looking to register to NASDAQ. Before the trip, he agrees to do a favor for his mother, Dr. Cathy Ryan, in which he will track down Aida Curić, her mother’s former patient, in the nearby city of Sarajevo in Bosnia. Aida, a Bosnian Muslim who escaped from her country during the Bosnian War, had her eyes cured by his mother twenty-five years ago.
After finishing his accounting job a week later, Ryan explores the city, especially the Triglav National Park, where he narrowly survives a murder attempt by a tourist known as Elena Iliescu. Unbeknownst to him, Iliescu is an assassin sent by a secret crime network called the Iron Syndicate, whose leader, Vladimir Vasilev, wanted Ryan, as well as ex-senator Weston Rhodes, eliminated as revenge for the death of his colleague Tervel Zvezdev. Rhodes was later killed in his prison cell.
Ryan informs his boss Gerry Hendley about the incident, who later learns about Iliescu’s connection to the Iron Syndicate from further investigation by Hendley Associates/The Campus head of IT Gavin Biery. He then sends The Campus to Europe in order to try to interrogate Iliescu; however, they find out that Elena was dead from a heart attack, silenced by the Iron Syndicate.
After being questioned by the Slovenian police about the incident, Ryan proceeds to Sarajevo to track down Aida. Initially failing in his efforts, he prepares for his flight back to the U.S. when Aida herself shows up in his rented apartment. Instantly smitten by her beauty, Ryan postpones his flight for a few more days and spends time with her, exploring most of Bosnia through a popular tour service that she owns; he even volunteers in a refugee agency that she also holds. They get into a fling for a few days. On the last night of his stay in Bosnia, Ryan and Aida encounter what Aida says are corrupt Serbian police officers (in fact they are Russian undercover agents searching for the stolen warheads). They manage to incapacitate them, which leads Ryan to believe something is amiss.
The next day, Ryan survives another murder attempt from an Iron Syndicate assassin in his rented apartment. He finally relents to Hendley’s persistent pleas and is about to fly home to the U.S. when he witnesses a plane being shot down by a surface-to-air missile, killing everyone aboard. Worried about Aida, he goes to her home, where he was abducted by the woman herself. Aida explains that she is part of her uncle Brkić's conspiracy plot and that she had ordered the attack on the civilian jet in order to kill Ryan, who had become a loose end. She then reveals the impending missile strike, which is on a Serbian Orthodox Church event in Sarajevo's Olympic soccer stadium, as she leaves Ryan under her cousin, who is also involved in the scheme, to prepare for the attack. Eventually, Ryan immobilizes him and escapes.
Ryan then tells his boss of the diabolical plot; his father, U.S. President Jack Ryan, his intelligence advisers, the military commanders based in Europe, and Russian President Nikita Yermilov are also informed. He tracks down Aida all the way to a dark tunnel, where he shoots her dead. He then proceeds to a nearby warehouse, where the forty thermobaric missiles are readied for launch. After informing Hendley of his location and engaging in a fistfight with Brkić's men, Ryan narrowly escapes just before the building is destroyed by a Tomahawk missile ordered by his father. The rest of the rockets are then retrieved by Russian and Bosnian intelligence operatives inside the stadium.
It was revealed that Red Wing is the Turkish ambassador to Bosnia. Ryan extracts a confession out of him, which was then uploaded to social media, humiliating him; he is later assassinated in an RPG attack. In the meantime, although Brkić escaped to Stockholm, Sweden, he was later killed in a mugging. Meanwhile, Vasilev was killed by The Campus in Paris, France, where he is recuperating from prostate cancer. Moreover, it was also revealed that the real Aida Curić was killed during the war in Bosnia after her eye surgery, and that the rest of her family was murdered by Bosnian mafia local head and Interpol fugitive Samir Kvržić, who wanted to change identities; the Aida that Ryan knew was actually Sabina Kvržić, his daughter. The Curić family's tour service was kept, but this time it was also used as a conduit to smuggle drugs, guns, and fugitives into the Balkans; when Samir died, his daughter took his place as the owner.