Crosscom 2.0 is an improvement on the original system introduced from the previous game, giving players more direct involvement in a combat situation as well as more control over friendly units.

Captain Scott Mitchell and his Ghost team are given orders to return to Mexico and continue opposing the rebellion, which has reached the Mexican state of Chihuahua and the border city of Ciudad Juárez.

General Joshua Keating informs Mitchell that apart from preventing an attack on U.S. soil, he must also investigate intel that suggests that the new rebel leader, Juan de la Barrera, is in possession of a dirty bomb.

Keating further adds that due to Congress not wishing to take military action, in addition to current international treaties between Mexico and the U.S., the Ghosts are officially not allowed to operate across the border and thus cannot be provided much support until America can legally enter the conflict.

Arriving in the mountains outside of Ciudad Juárez, Mitchell begins assisting loyalist Mexican Army soldiers, led by Colonel Jimenez, in attacking rebel positions.

Though the Ghosts successfully extract the journalist, their transport, Blackhawk 5, is shot down by mercenaries assisting the rebels, and they are forced to abandon Lieutenant Rosen.

Soon after being extracted, Barnes reveals that the rebels managed to secure Blackhawk 5's crash site before they could, removing both the wreckage and an injured Rosen, in order to manipulate the media and expose America's illegal involvement against the rebellion, thus gaining support for their cause.

The Ghosts use the rescued journalist's information to begin tracking down the two missing warheads, killing de la Barrera in the process, but only manage to neutralize one.

Intelligence eventually reveals that the mercenaries have launched an attack on a dam within El Paso, Texas, prompting fears that the warhead will be detonated on U.S. soil.

However, Barnes reveals that the true target was a highly classified military installation beneath the dam that is connected to the United States anti-ballistic missile defense grid.

Keating surmises that by dropping the grid, de la Barrera intended to nuke major American cities in the hopes of forcing them out of Latin America.