In early 1928, the Schneider Trophy rules were changed. It was agreed that it should be held every two years instead of annually in order to provide more time for competing nations to build and test their new machines. This was a great help to Mitchell as he readied himself for the defence of the Trophy at Cowes.
When beginning work on the design for the Supermarine S.6, Mitchell made an important decision, one that he had held back on in 1927. He felt that the Napier Lion engines, although always reliable, had been developed to their limit. He decided he needed a new manufacturer and sought the advice of Maj. GP Bulman, an Air Ministry official responsible for the development of aero-engines. Bulman confirmed his thoughts, Mitchell approached Sir Henry Royce, and so began a partnership between Supermarine and Rolls-Royce that was to prove invaluable, not only in the creation of race engines but later in the production of both the Merlin and Griffin engines that so successfully powered the Spitfire.
Rolls-Royce provided assurances that they could supply an engine of at least 1,500hp, with development up to 1,900hp, and, most importantly, little or no increase in frontal area. Supermarine gave Rolls-Royce only six months to produce the power unit and the result was a fully tested "R" engine.
Mitchell designed the S.6 around the basic streamlined shape of the earlier S.5, moving the floats forward to carry the extra weight of the "R" engine when on water. Because of the increased fuel consumption both floats were designed to serve as fuel tanks and, with the increased engine heat, the surface of the wings and floats were used as radiators for cooling.
In February 1929, a new RAF High Speed Flight was formed and on 5th August the S.6 was towed to Calshot for its leader, Sqd Ldr AH Orlebar, to undertake the first test flight. Unfortunately he was unable to get airborne as the plane swung violently to port. The engine's torque forced the port float to dig into the water and the plane pivoted around it. This was quickly counteracted by carrying most of the fuel in the starboard float.
As holders, the British decided that the 1929 Schneider Trophy was to be held at Cowes. The course comprised a four-sided 50km lap starting and finishing off Ryde pier. The turning points, off Seaview, Hayling Island and Cowes, were marked by pylons painted yellow and black and mounted on destroyers. The British pilots were again issued with similar lap recorders to the 1927 race; seven paper covered holes in a piece of board, which were pushed through as they completed each lap.
On 7th September, race day, crowds flocked to vantage points on both sides of the Solent, as well as on boats and ships anchored all along the course. It was estimated that 1.5 million spectators came to see the spectacle. Only Italy (with two Macchi M.67s and an older Macchi M.52R) had sent a team to compete against the British entry of two S.6s, N247 and N248, flown by Flg Off "Dick" Waghorn and Flg Off "Batchy" Atcherley respectively, and an S.5, N219 flown by Flt Lt D'Arcy Greig.
Britain had drawn first (Waghorn), third (D'Arcy Greig) and fifth (Atcherley) starting positions. The large collection of ships moored in the Solent made the spotting of the Seaview and Hayling pylons difficult for the pilots and Waghorn flew a cautious first lap to avoid missing a turn. His first lap was recorded at 324mph. Atcherley was disqualified for allegedly cutting inside a pylon on his first lap and the two Macchi M.67s retired on the second lap with engine trouble leaving only the older Macchi M.52R to compete. The M.52R was no match for the speed of the S.6, until, on the last lap, Waghorn's engine cut out. It picked up again slightly and so he climbed to a height of around 800ft in the hope that if it stalled again he could glide over the finishing line. As he rounded the Cowes pylon it stopped altogether and he was forced down on to the water. He felt cruelly disappointed to lose the race with victory in sight but was elated to discover, when the rescue launch arrived, that he had in fact won. He had miscounted his laps, exactly as Webster had done in 1927, and had already completed the course when the engine ran out of fuel.
Waghorn had finished first with an average speed of 328.26mph, Dal Molin in the Macchi M.52R was second at 284.2mph with D'Arcy Greig's S.5 in third place, just behind him, at 282.11mph.
A story is told of Mitchell's reaction when he first heard that Waghorn had won the Schneider Trophy. As he stepped off of the launch and walked up the Calshot slipway, a Supermarine man moved forward to shake his hand saying, "Congratulations, sir. I am pleased we have won for your sake." To which Mitchell replied, "Thank you, but it is not really for my sake, you know, it is for our country's."