John Marston first comes across the Mexican Army during the mission "Civilization at any Price", which is led by Colonel Agustin Allende, Major Raul Zubieta, Captain Vincente de Santa, Captain Espinoza and overseen entirely by General Ignacio Sanchez.

Marston agrees to help the Army fight the Rebels throughout Mexico, in return Colonel Agustin Allende tells Marston that while Marston fights alongside the Army, the Army will search for their leader, Abraham Reyes, which in turn will lead them to Javier Escuella, which is the reason why Marston is in Mexico.

While in Mexico, John Marston helps the Army fight the Rebels, until Captain De Santa tells John they have captured Javier Escuella; De Santa tells Marston that Escuella is being held in the local church in Chuparosa. Upon arriving in Chuparosa, the Army attacks Marston and prepares to execute him. Just as the Army prepares Marston for execution, Abraham Reyes alongside his Rebels attack Captain Espinoza and his troops. After releasing Marston, the rebels continue to attack the soldiers until Colonel Agustin Allende and the remainder of his soldiers are killed. This is the last mission Marston fights for the Mexican Army.

General Ignacio Sanchez, his top ranking officers, and his Army are eventually overthrown by Reyes' Rebels. After Marston leaves Mexico, this is the last mission directly involving the Mexican Army.