The United States and the Republic of China had a long history of joint clandestine efforts against mainland China beginning in 1955 with project HUNTING WOLF. In 1957 the RB-69A Neptunes were sent to replace the aging ROCAF B-17s previously used for ELINT work. The RB-69As were loaned to the ROCAF 34th Squadron, 8th Group, operating from Hsinchu Air Base, which also served as U.S. Headquarters for the project. No markings were carried on the ROC Neptunes other than a removable placard on the vertical tail bearing a ROCAF number. Some Neptunes carried four aft-facing AIM-9B "Sidewinder" missiles on wing pylons.
The 34th Squadron, nicknamed the "Bats", flew most missions at night, below 1,000 feet. In addition to the ELINT snooping and leaflet drops, the RB-69As flew night missions to drop agents by parachute. Over-flights of communist Chinese territory were routine and comparatively safer than Europe, since China had not yet established a sophisticated SAM defense network. More than 80 penetrations of Chinese airspace were flown from 1958 through the mid 1960s. Missions were also flown over North Vietnam. In time the Mainland Chinese improved their air defenses, which began to take its toll on the small group of Neptunes.
From 1960 to 1964, all five of the original batch of RB-69As were either lost to hostile actions by the Communist Chinese or to operational accidents. Two aircraft were transferred from the Navy inventory to replace the lost aircraft. The last two Neptunes were finally withdrawn from service in 1965-1966 and returned to the continental US and into Navy ranks once more. Both airframes would continue to be involved in special testing until being retired to Davis-Monthan.