'On 19 January 1801, a commission was signed at the Admiralty appointing me Lieutenant of His Majesty's sloop Investigator to which the name of the ship, heretofore known as the Xenophon, was changed by this commission ... I took the command at Sheerness on the 25th of the same month.
     The Investigator was a north-country ship, of three hundred and thirty-four tons; and, in form, nearly resembled the description of vessel recommended by Captain Cook as best calculated for voyages of discovery. She had been purchased some years before into His Majesty's service; and having been newly coppered and repaired, was considered to be the best vessel which could, at that time, be spared for the projected voyage to Terra Australis ... 
     The compliment of the Xenophon had been seventy-five men; but on the name and destination of the ship being changed, the following establishment was ordered. The names of the officers are added to the list, and also of the men of science who took part in the expedition, which left the whole numbers of persons on board to be eighty-eight, at the time of sailing.'
- Matthew Flinders in Terra Australis


However, the Investigator, a converted collier (coal carrier), did not fare well on the long voyage from England (1801), and problems were noticed in northern Australia (during the circumnavigation voyage). While in the Gulf of Carpentaria in late 1802 the ship was leaking sufficiently to warrant repairs. At this time, the carpenter, upon inspection of the timbers found that some were rotting. The ship was only marginally seaworthy, and would need major repairs in the near future. This was a devastating blow to Flinders, and along with health problems of the crew, forced the shortening of the coastal survey and exploration. The Investigator began to take in so much water that if the ship had sailed into rough weather she may well have sunk. The ship was in a terrible state by her return to Sydney in June 1803. Many of the planks of the hull were rotten and in need of replacement. A thorough inspection by the Master builder to the Territory of New South Wales and captains of two other ships revealed that the ship was unfit for further service on return to Sydney. They stated:


' ... being the state of the Investigator thus far, we think it altogether unnecessary to make any further examination; being unaminously of the opinion that she is not worth repairing in any country, and that it is impossible in this country to put her in a state fit for going to sea.'
- Matthew Flinders in Terra Australis


This, of course, was a terrible blow to Captain Flinders, who had not completed the survey of the Australian coastline to his own satisfaction. He had hoped to fill in the remaining gaps. Thus another ship had to be found for this. As no ship in Sydney was suitable, it was necessary  for Flinders to return to England to find another ship, taking his notes and charts with him. 

Matthew Flinders' Australian adventures had not yet finished; the intended trip home included both tragic and heroic events. There was a ship wreck and a rescue. And the long, bitter imprisonment by the French. Matthew Flinders should have been able to return home acknowledged as a great explorer, but this was not to be ... (but that is another story).

... And another story  involves the Investigator herself, after she had been decommisioned. Captain Flinders had left her as a hulk, moored in Port Jackson after the conclusion of the great voyage of circumnavigation (1801-1803). However, in 1804, Governor King had another inspection carried out, and the conclusion was that with work, including the lowering of the ship by removing the top deck ('cutting down'), and re-rigging, the Investigator could sail again. 

The alterations were made, and the lowered ship sailed for England in 1805. She encountered bad weather and overall, the voyage was difficult and unpleasant. The botanists Robert Brown and Ferdinand Bauer, two of Flinders' scientists, were on board, with the collections from their expeditions in Australia. Ironically, they left Sydney after Flinders, but reached England years before him. Of course, news of the Investigator's return to England did not sit well with Matthew Flinders, who was in prison at Mauritius ... (but that, too, is another story).

The cut-down Investigator still continued to work for some time after the return to England. Eventually she sailed for the final time, was decommisioned (again) and was broken up for the materials that still remained useable ... an inglorious end for such a hard-working and important vessel. Imagine how famous the Investigator would now be if she had been sent to a museum for preservation and display - but at that time history was not viewed in the way it is today.