At the outbreak of the Second Anglo-Maratha War, in 1803, Lieutenant John Vaughan received orders to raise a battalion of sepoys in the area of Fatehgarh for the purpose of adding a new regiment to the establishment.

At the departure of the commander in chief, General Lord Gerard Lake to England in 1807, his Excellency recognised the role of the 21st N. I. with a letter were stated "I shall ever remain grateful for the important services, which in the course of the war, were rendered by the officers of the 21st regiment of Native Infantry".

In April 1815, at the final period of the Napoleonic Wars, the British Sovereign appointed some senior general officers serving in India Knight Commander of the Order of the Bath.

At the end of 1815, Captain Vaughan is intrusted to bring from London the insignias intended of the Knights Commander of the Order of the Bath resident in India to Calcutta on board the H. C. Ship Carnatic.

In this capacity he accompanied Francis Rawdon-Hastings, 1st Marquess of Hastings, then Governor-General and commander in chief, in the Centre Division for the whole campaign of the Grand Army.

15 November 1824, Lt-Col. Vaughan was nominated a member of the Special Court of Enquiry ordered by the Government of India under instruction of the commander in chief, to investigate the causes and deal with the first sepoy mutiny at Barrackpore (2 Nov. 1824).

In 1828, Vaughan was promoted to Lieutenant-Colonel Commandant, 8 February, and again chosen, on 13 March, to be supernumerary Aide-de-Camp to the acting Governor-General, now William Butterworth Bayley (later chairman of the British East India Company).