The discovery of the murder of an American businessman, Peter Hardin, and his family, outrages U.S. President Edward Bennett (Donald Moffat), Hardin's personal friend. When Hardin is found to have been connected to a Colombian drug cartel, from which he skimmed over $650 million, Bennett tells James Cutter (Harris Yulin), his National Security Advisor, that the cartels represent a "clear and present danger" to the United States, tacitly instructing him to use force against the men responsible for his friend's murder. Jack Ryan (Harrison Ford), appointed acting Deputy Director of Intelligence after Vice Admiral Jim Greer (James Earl Jones) is stricken with cancer, asks Congress for increased funding for ongoing CIA operations in Colombia, believing the funds to be for advisory purposes only. Congress is concerned that the FBI has asked for similar funding increases in the past to carry out covert military ops against state enemies. But Ryan gives a personal assurance that that's not the case. $75M is issued. Keeping Ryan in the dark, Cutter turns to CIA Deputy Director of Operations Bob Ritter (Henry Czerny) to take down the cartel. Ritter insists on Cutter giving him a written authorization before he conducts any covert operations on foreign soil. Ritter assembles a black operations team code-named RECIPROCITY with the help of John Clark (Willem Dafoe). Clark also knows this is black ops and demands payment into his bank account before he moves. The whole thing has been hidden from the U.S. Congress. The team inserts itself into Colombia, with Clark running logistics and Captain Ricardo Ramirez (Benjamin Bratt) of an SF-ODA team commanding the squad on the ground in clandestine search-and-destroy missions against the drug cartel. Their team carries out several hits on planes full of drugs, planning to ship to the U.S. All of them belong to Escobedo. Ryan finds that 3 years ago, Hardin received a large infusion of foreign capital that he invested in shopping malls in the U.S. and posted record profits. It is clear to Ryan that Hardin was laundering money for the Columbian drug cartels. Meanwhile, Bennett sends Ryan to Colombia to investigate Hardin's cartel connection and also to retrieve the $650MM sitting in Hardin's offshore accounts. Ryan would need to establish who Hardin was working for before the U.S. Govt. could seize the money. Greer knows that Ryan has been trapped and tells him to lean on Clark in case he gets into a mess. Jean Fowler (Belita Moreno) is the FBI officer in charge in Bogota and tells Ryan about Escobedo's operations, including Cortez (for whom they don't have a picture). Ryan meets Clark, but Clark doesn't tell Ryan about the hits. Clark takes Ryan seriously when he says he is Greer's man. The cartel leader responsible for Hardin's murder, Ernesto Escobedo (Miguel Sandoval), is enraged when the U.S. attempts to claim the $650 million that was stolen from him and has his intelligence officer, Félix Cortez (Joaquim de Almeida), try to retrieve the funds. Cortez did not agree with Escobedo's strategy to kill Hardin since he was a politically connected figure in the U.S. Cortez visits the U.S. and has a new connection, Moria Wolfson (Ann Magnuson), whom he uses as cover for his spying activities. Cortez is careful to hide himself from Moria's friends whenever he meets her. Moria is on Jack Ryan's FBI team investigating the Hardin murders. Meanwhile, Ramirez's team starts cleaning out Escobedo's cocaine factories hidden in the jungles. Bennett sends FBI Director Emil Jacobs (Tom Tammi) to meet Ryan in Colombia and negotiate with the Columbian Govt. for the money (after Ryan had told Bennett that the link between Escobedo and Hardin was established (Hardin was buying coffee from Escobedo, but was paying $6200 per pound), but Columbia would want to keep a large portion of the funds), and when Cortez discovers this (from Moria, whole unwittingly discloses Jacobs plans to Cortez), he plans an ambush, engineering it so that suspicion will fall on Escobedo. Ryan barely escapes the ambush by cartel hit-men (Cortez kills Moria after travelling to the U.S.), but the remainder of the entourage is killed. Ryan returns to the U.S. Escobedo then summons a meeting with other cartel leaders, which Clark's team hits with an airstrike, but Escobedo arrives late and survives. Several women and children also die in the attack. Ryan finds it strange that Moria was killed the same day as Emil. He checks her answering machine and finds a recorded message from a Latin sounding guy. Sound analysis provides a match with Cortez. Ryan also finds that Ritter ordered the airstrike on the cartel meeting. Cortez discovers the American involvement in the strike and meets with Cutter (he faxes Cutter that he knows American troops are in Columbia fighting an illegal war and threatens to expose it) to broker a deal (the meeting happens in Panama). Cortez will assassinate Escobedo and take over the cartel, promising to reduce drug shipments to the U.S. and allow American law enforcement to make regular arrests to make it appear as if the U.S. is winning the drug war. In exchange, Cutter will shut down all U.S. operations in Colombia and allow Cortez to hunt down Clark's soldiers. Cutter agrees and orders Ritter to get rid of all evidence of their operations and cut off the troops in Colombia from all support. Ryan is played a recording of the conversation between Cutter and Cortez. He hacks Ritter's computer and discovers the conspiracy unfolding in Colombia. The Reciprocity team is ambushed in Colombia by Cortez's mercenaries. Ritter had shut down the satellite link so Clark could not contact the men as they screamed for help. Cutter and Ritter tell Clark that Ryan found out everything and threatened to expose them if they didn't shut it down. They say that Ryan is on his way to Bogota, and if Ryan is out of the way, they are back online. Basically, Ritter and Cutter recruit Clark to kill Ryan for them. Ryan arrives and convinces Clark to allow him to help. Clark calls Ritter and says he killed Ryan and wants the satellites turned back on. But Ritter hangs up on him, proving Ryan's point. They find the team's sniper (Ryan buys a helicopter for $2M and goes searching in the jungles with Clark), Chavez (Raymond Cruz), who tells them that Ramirez and a squad mate have been captured and the remainder have been killed. Ryan visits Escobedo's mansion and shares his intelligence on Cortez. Enraged, Escobedo confronts Cortez but is killed by Cortez's associate. Ryan, Clark, and Chávez rescue the prisoners, kill Cortez, and escape. Ryan confronts the President and tells him he intends to inform the Congressional Oversight Committee about the conspiracy despite the damage it could do to his career. As he walks out of the Oval Office, Cutter asks to speak with him, but Ryan ignores him. Ryan then begins his testimony to Congress.
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