Nelson was stripped of his clothes and his body hair was removed before the his was placed inside a water leaguer. The water leaguer was used as there was not enough lead on board to make a coffin. The leaguer was then filled with brandy (not rum as is often thought) to preserve the body. A water leaguer could contain 184 gallons of water and was the largest barrel on board ship of Nelson's time.

The leaguer was placed on the middle gun deck of HMS Victory and guarded by Royal Marines. During the voyage to Gibraltar the brandy was drawn off and the leaguer refilled.

Victory arrived in Gibraltar on 28th October, this short journey taking seven days due to the very poor weather conditions, rough sea state and high winds. Whilst in Gibraltar the brandy was again drawn off and the leaguer was filled with a solution of two parts brandy and one part spirit of wine. This procedure was carried out twice on the passage from Gibraltar to England.

HMS Victory sailed for England on the 4th November 1805, was with Vice Admiral Collingwood off Cadiz until the evening of the 5th and then continued her journey home.

Victory arrived off St Helens on the 4th December 1805 and moved to Spithead on the 5th. The ship remained at anchor till the 10th of December when she sailed for the Nore. At this time Nelson's body was taken from the leaguer for inspection and Surgeon William Beatty removed the bowels which had started to decay and would have putrefied the rest of the body.

Whilst examining Nelson's body Doctor Beatty found the musket ball which killed Nelson. It had passed through the spine and lodged in the muscles of the back towards the right side, a little below the shoulder-blade.

The report by Surgeon Beatty on Nelson's wound:

"The ball struck the fore part of his Lordships' epaulette; and entered the left shoulder immediately before the processue acromion scapulæ, which it slightly fractured. It then descended obliquely into the thorax, fracturing the second and third ribs: and after penetrating the left lobe of the lungs, and dividing in its passage a large branch of the pulmonary artery, it entered the left side of the spine between the sixth and seventh dorsal vertebræ, fractured the left transverse process of the sixth dorsal vertebra, wounded the medulla spinalis, and fracturing the right transverse process of the seventh vertebræ, made its way from the right side of the spine, directing its course through the muscles of the back; and lodged therein, about two inches below the inferior angle of the right scapuld. On removing the ball, a portion of the gold-lace and pad of the epaulette, together with a small piece of His Lordship's coat, was found firmly attached to it."

"W.Beatty."

Lord Nelson's remains were wrapped in cotton vestments, and rolled from head to foot with bandages, as in embalming. The Body was placed into a lead coffin, filled with brandy holding solution of camphor and myrrh. The lead coffin was then placed inside of a wooden one, and then taken to Lord Nelson's cabin until the 23rd December 1805.

The Admiralty had ordered that the yacht Chatham III which was the Honourable George Grey's the (Commissioner at Sheerness Dockyard) should carry the body of Nelson from HMS Victory to Greenwich.

From the log of HMS Victory 23rd December 1805:

"At 1-40 shortened sail and anchored with Small Bower in 12 fathoms.... in the Swin. Moored ship. Came alongside Commissioner Grey's Yacht from Sheerness, and recieved the remains of the late Lord Viscount Nelson K.B. and Vice Admiral of the White. Got a piloton board to take the ship to Chatham."

The body was removed into the coffin made from part of the wreck of the ORIENT, burnt at the Battle of the Nile, and presented to Lord Nelson by Captain Hallowell of the SWIFTSURE, in 1799. This coffin with its contents was placed within a leaden coffin. The latter was soldered, and never afterwards opened. On the coffin being lowered into the yacht, the Victory struck, for the last time, Lord Nelson's flag at the fore and the same was hoisted half-mast high on the yacht.

The records of the log were taken from "British Royal Yachts A Complete Illustrated History" by Tony Dalton.

The Yacht Chatham arrived off Greenwich on the 24th December at 2pm, on her journey up the River Thames all military honours were paid. At 7pm Lord Nelson's body was taken through the centre gate from the river into the Royal Hospital.

From Bell's Weekly Messenger November 17th 1805

Nelson's coffin at Mr Pedderson(Undertaker)
Brewer Street
Golden Square
London

The coffin which will contain the body is made out of the mast of L'Orient French ship which blew up. A brass engraved plate, with an inscription to the effect is fixed on the lid of the coffin. From the shape, it appears to have been made at sea, by a ships carpenter, the shoulder's being square, instead of the usual way made by Undertakers. The substance about an inch thick, is covered with fine black, the inside lined with superfine crape, and the ruffling, pillow, mattress, and sheets, is white satin. This coffin, which is extremely plain will be placed into a leaden coffin, and the whole will be put into an oak case, covered with crimson or black velvet, and finished with guilt furniture.