Despite the downfall of Carlos Ontiveros and his coup in Mexico City, rebellion across Mexico continues unabated, spreading civil unrest across the country and into other Latin American countries, including Colombia, Honduras and Panama, with the Panama Canal effectively shut down by the rising insurgency in Latin America. Although having only recently returned to the United States, Captain Scott Mitchell is given new orders to return to Mexico with a team of the elite Ghost Recon force, and continue fighting against the rebellion, which recently entered the Mexican state of Chihuahua and the bordering city of Ciudad Juárez. General Joshua Keating, the Ghosts' commander, informs Mitchell that, apart from preventing the rebels from directly assaulting U.S. soil, he must also investigate recent intel that suggests that the new leader of the insurgents, Juan de la Barrera, a man opposed to the signing of the North American Joint Security Agreement (NAJSA) and to American involvement in Latin America, is in possession of a dirty bomb of either nuclear, chemical or biological origin. Keating further adds that due to Congress not wishing to take any military action against the rebels, along with current international treaties between Mexico and the U.S., the Ghosts are legally non-existent across the border and thus cannot be provided much support until America can legally enter the conflict.