In March 1965, it was designated the primary aircraft for performance, stability and control tests. On 21 October, Article 2004 was flown to nearby Edwards Air Force Base to join the SR-71/F-12 Test Force. The Test Force conducted flight evaluations of the triple-sonic spyplane, its systems and sensors. The organization was responsible for obtaining performance and handling qualities data for inclusion in the SR-71 flight manual. Lockheed personnel performed the majority of envelope expansion flights, while the Air Force devoted its major effort toward validating predicted data and obtaining quantitative performance and handling qualities data.
Category II tests began on 9 November 1965. Testing was conducted under the authority of Headquarters, Air Force Systems Command, with a priority of 01. Preliminary test data was forwarded to Lockheed's Advanced Development Projects division and the SR-71/F-12 Systems Program Office for inclusion in the flight manual.
On 29 July 1966, after 19 missions, Article 2004 was removed from flight status for installation of improved engines and a modified nose section. As a result of the modifications all test data obtained with the original nose and engines were invalidated in regards to category II testing.
Flight-testing resumed on 6 October 1966 and from that date until 1 January 1967 the Test Force concentrated on obtaining a limited amount of cruise data at between Mach 2.4 and 3.0. The airplane had not yet been cleared for extended operation at Mach 3.2, the design cruise speed.
Although the Category II test program was officially concluded in June 1967, the performance, stability and control tests were not complete. Mach 3.2 cruise tests were finally accomplished in the latter part of 1967 through 8 July 1968. Overall, a total of 87 Category II performance, stability and control sorties were flown, totaling 177 flight hours. On one mission the airplane attained an altitude of 86,700 feet.
On 11 July, Article 2004 was returned to Lockheed for scheduled maintenance and installation of a new classified defensive avionics package.