Throughout 1959, English Electric (EE) and Vickers worked on combining the best of both designs in order to put forward a joint design with a view to having an aircraft flying by 1963, while also working on merging the companies under the umbrella of the British Aircraft Corporation (along with Bristol Aircraft). EE had put forward a delta winged design and Vickers, a swept wing on a long fuselage. The EE wing, born of their greater supersonic experience, was judged superior to Vickers, while the Vickers fuselage was preferred. In effect, the aircraft would be built 50/50: Vickers the front half, EE the rear.
The TSR-2 was to be powered by two Bristol-Siddeley Olympus reheated turbojets, advanced variants of those used in the Avro Vulcan. The Olympus would be further developed and would power the supersonic Concorde. The design featured a small shoulder-mounted delta wing with down-turned tips, an all-moving swept tailplane and a large all-moving fin. Blown flaps were fitted across the entire trailing edge of the wing to achieve the short takeoff and landing requirement, something that later designs would achieve with the technically more complex swing-wing approach. No ailerons were fitted, control in roll instead being implemented by differential movement of the slab tailplanes. The wing loading was high for its time, enabling the aircraft to fly at very high speed and low level with great stability without being constantly upset by thermals and other ground-related weather phenomena. The EE Chief Test Pilot, Wing Commander Roland Beamont, favourably compared the TSR-2's supersonic flying characteristics to the Canberra's own subsonic flight characteristics, stating that the Canberra was more troublesome.
According to the Flight Envelope diagram, TSR2 was capable of sustained cruise at Mach 2.05 at altitudes between 37,000 ft (11,000 m) and 51,000 ft (16,000 m) and had a dash speed of Mach 2.35 (with a limiting leading edge temperature of 140 degrees Celsius). Its theoretical maximum speed was Mach 3 in level flight at 45,000 ft (14,000 m).
The aircraft featured some extremely sophisticated avionics for navigation and mission delivery, which would also prove to be one of the reasons for the spiralling costs of the project. Some features, such as forward looking radar (FLR), side-looking radar for navigational fixing, only became commonplace on military aircraft years later. These features allowed for an innovative autopilot system which, in turn, enabled long distance terrain-following sorties as crew workload and pilot input had been greatly reduced.
There were considerable problems with realising the design. Some contributing manufacturers were employed directly by the Ministry rather than through BAC, leading to communication difficulties and further cost overruns. Equipment, an area in which BAC had autonomy, would be supplied by the Ministry from "associate contractors", although the equipment would be designed and provided by BAC, subject to ministry approval. The overall outlay of funds made it the largest aircraft project in Britain to date.
Unlike most previous projects, there were to be no prototypes. Under the "development batch" procedure pioneered by the Americans (and also used by English Electric for the Lightning), there would instead be a development batch of nine airframes, to be built using production jigs. The choice of proceeding to production tooling turned out to be another source of delay, with the first aircraft having to adhere to strict production standards or deal with the bureaucracy of attaining concessions to allow them to exhibit differences from later airframes. Four years into the project, the first few airframes had effectively become prototypes in all but name, exhibiting a succession of omissions from the specification and differences from the intended pre-production and production batches.