The full plot of Clear and Present Danger turns on one betrayal: the people running a secret war in Colombia decide to abandon their own team. Here it is in steps.
1. The hidden operation. The President secretly lets his national security advisor, James Cutter, set up an illegal military operation in Colombia. Ryan gets funding approved without knowing it is paying for this hidden force. The field operative John Clark recruits and leads the team in the jungle.
2. The ambush in Bogota. Ryan travels to Colombia on a diplomatic mission. The cartel's intelligence chief, Felix Cortez, has his convoy ambushed in Bogota, and several of Ryan's colleagues die.
3. The counterstrike. The hidden team retaliates by bombing a cartel meeting, but Escobedo and Cortez survive.
4. The double cross. Cortez makes a deal with Cutter. He will take over the cartel, and in return Cutter must abandon the team and give up its location. The team is left stranded and hunted.
5. Ryan finds out. Back on his own trail, Ryan finds proof of the illegal operation, and he learns that the President and the officials involved have been promised pardons.
6. Ryan and Clark. Ryan goes to Colombia to find Clark, who at first believes Ryan betrayed him. Once they work out that they were both lied to, they join forces and free the captured team members from a cartel compound.
7. The escape. Escobedo is killed, and Domingo Chavez kills Cortez during the escape.
8. Washington. Back in Washington, Ryan refuses the President's request to help hide the scheme and agrees to testify before Congress.