Taking place just after Island Thunder the Jungle Storm campaign is set in Bogotá, Colombia, the drug cartel that had aided and financed the FDG in their efforts in Cuba, the FARC, has initiated a number of terrorist attacks against the Colombian government who has allied themselves with America. After Colombia's call for help following an attack on a U.S. Embassy, America responds by deploying the Ghosts to restore order and put the cartel out of business. Once deployed, the Ghosts mobilize to face off with a newly-formed militia group called the MFLC (Movimiento de las Fuerzas Libres Colombianas), which is basically the southern equivalent of the FARC. The chaos caused by the MFLC is spreading into Ecuador and Peru, making the peacekeeping effort especially vital. Throughout the campaign, the Ghosts hunt down several of the MFLC's leaders, defend civilian centers spread throughout the region, free civilian prisoners, and cut off the flow of drugs in order to deny the MFLC financial backing. Although the Ghosts cause massive damage to the MFLC's war efforts, the MFLC and the FARC have connections to sleeper cells holed up in democratic Cuba. Unless they are told to hold back their use of force by their commanders in Colombia, they will cause widespread damage to Cuba and its populace. To prevent this senseless act of violence, the Ghosts assault the last major MFLC campsite in the hills, which surrounds a large radio tower. With the help of U.N. peacekeepers and captured personnel at the tower, the Ghosts shut down the sleeper cells in Cuba, paving the way for them to strike at the heart of the MFLC and ending their rebellion permanently. The game goes into little detail as to what happens after the MFLC are defeated, but supposedly their defeat shuts down the rebellion put up by the other rebel factions and the FARC across Colombia.
Source: Wikipedia, Tom Clancy's Ghost Recon: Jungle Storm , available under the CC-BY-SA License.