In 1903 he settled with his family at Bramdean House in
Alresford, and was appointed Commander of the Balloon Sections, based at
Aldershot under the command of Col
James Templer. In October 1905 he was promoted to lieutenant colonel, and to brevet colonel in January 1906. Later that year, having briefly become the Balloon Companies, the organisation became the
School of Ballooning with Capper, who in January that year had been promoted to brevet colonel, as its commandant. At about the same time the Balloon Factory was split off and moved to a new site nearby at Farnborough and, on Templer's retirement, Capper also became its Superintendent and was given the brevet rank of full
colonel. Templer was retained at the factory under Capper to complete the development of Britain's first military airship, the
Nulli Secundus ("second to none") in a purpose-built airship shed. Capper not only supervised the British Army's ballooning and airship activities, but took a wider interest in aeronautics. In anticipation of the new airship, he took up the civilian sport of ballooning, flying in competitions initially as assistant to the
Hon. C.S. Rolls and later with his own balloon "Pegasus" and his wife as assistant. Capper and Cody undertook the first successful flight of a British airship, the
Nulli Secundus, over
London in 1907. Capper went on to modify the airship as
Nulli Secundus II, parodied by
Punch as "second to none the second", and a smaller experimental airship called
Baby. Neither was an immediate success, although
Baby would later be modified and have a long and successful career. Capper oversaw the first Army aeroplanes. He briefly flew Dunne's first glider, the
D.1, during secret trials at
Blair Atholl in Scotland in 1907. The flight had lasted only a few seconds when the glider crashed into a wall, with Capper sustaining a cut to the head. The next year, Cody flew the first British-built aeroplane at Farnborough, which earned it the title
British Army Aeroplane No.1. This was an ironic achievement for Capper's command, as he had pinned his personal hopes on Dunne, whose
D.4 achieved no more than a few hops. That autumn the government conducted a formal inquiry into military aviation. Capper had to return early from Blair Atholl in order to present his evidence. He argued strongly for a promising future of all forms of aeronautics and especially the aeroplane. However his Army superiors on the committee were against aeronautics in any form. It was decided that only small-scale airship experiments should continue and that aeroplane work should be stopped. It formally ceased when Dunne and Cody's contracts ran out at the end of March 1909. Soon afterwards the Balloon Factory was removed from the command of the army and a new civilian superintendent,
Mervyn O'Gorman, appointed. Capper remained in command of the Army Balloon School. When Dunne left Farnborough, Capper was one of several friends who offered support for his efforts. In 1911, one of Dunne's new aeroplanes was exhibited at the Olympia Aero Show, with a placard stating it was "Built to the order of Col. J. E. Capper, R.E." He relinquished this position in October 1910 and was placed on
half-pay, and promoted to colonel. In April 1911 he was transferred to the
School of Military Engineering at
Chatham as its new commandant, marking the end of his aeronautical career. ==First World War==