An aggrieved first term President implicitly ("What I would suggest I cannot suggest") authorizes a secret military incursion into Columbia after a personal friend of his is killed by men connected to Ernesto Escobedo, leader of the Cali Cartel. Jack Ryan, temporarily promoted as Deputy Director of Intelligence at the CIA after Jim Greer is diagnosed with cancer is unintentionally mired in the scheme. He was tasked with securing the funding for the operation from Congress, even specifically promising no troops would be used despite that being (unbeknown to Ryan) the whole point of the operation.
The military operation is initially successful, striking at drug refining facilities and shooting down drug running aircraft. After the President orders a large amount of laundered drug money seized, Felix Cortez, a former Castro official working as an intelligence officer for Escobedo, retaliates by assassinating a Presidential aide (from which Ryan himself narrowly escapes) sent to Columbia to discuss the seized funds with the Columbian government. After that, the operation is escalated and the US troops are ordered to begin assassinating cartel leaders themselves, who have met to assuage their own suspicions that each other are responsible for the strikes by US troops and avert a gang war.
In response, Cortez figures out that American troops have been operating in Columbia and negotiates their betrayal with the President's National Security Advisor (Cutter) who orchestrated the unconstitutional operation.
Meanwhile, Ryan has also caught on that something illicit is happening and catches the basic gist of the operation after breaking into a colleague's office computer at CIA. He is too late to prevent the betrayal of the US soldiers in Columbia who are captured after their exact location is given to Cortez and all air support and communications with them are cut off. Ryan personally returns to Columbia to organize a rescue operation, which he cobbles together with the help of a disgruntled CIA operative who had been involved in the military operation itself.
Ryan returns to Washington DC, to reveal all details of the operation to Congress even after the President personally tries to entice him to remain silence with offers of future favours.