Cojuangco was a close adviser and personal friend to former Philippine President Ferdinand E. Marcos, which led his estrangement from his cousin, Corazon Aquino, who, after Marcos' ouster, succeeded him as President. He was a member of the group nicknamed the "Rolex 12", a group of 12 men who were closest to Marcos and allegedly were his enforcers of Martial Law. He is also an honorary member of PMA Class 1951. Cojuangco also was accused by the military men at the scene of Benigno Aquino Jr.'s assassination, as the leader who orchestrated the crime.