According to strict orders from the Admiralty, Cook on 30th September collected all logs and journals that had been kept on board the ship, and enjoined every one that they were on no account to divulge where they had been on their arrival at Batavia.  Off Java Head the main topsail was split in a squall, and Cook remarks that all his sails are now in such a condition that “they will hardly stand the least puff of wind.”  No observations had been possible since leaving Savu, and the strong western current had thrown out their dead reckoning, causing them to run past the Straits of Sunda; but, picking themselves up on 1st October, they got into the straits, and after a wearisome beat up arrived in Batavia on the 10th; and Hicks was sent on shore to announce their arrival, and offer an apology for failing to salute the Dutch flag in a proper manner—­the reason being that they had only three guns available.

The ship was thoroughly surveyed, and on the carpenter’s report, Cook applied to the Governor for a convenient place in which to heave down and repair, and for permission to purchase such stores as might be necessary.  Every assistance was promised, and on Cook’s finding a difficulty in getting any private person to cash the bills he would have to draw for his expenses, the Governor ordered the officer in charge of the port to supply whatever amount might be necessary.

During a heavy thunderstorm on the 12th, a Dutch East Indiaman, about two cables away from the Endeavour, had mainmast “split all to shivers.”  The Endeavour was also struck: 

“and in all probability we should have shared the same fate as the Dutchman, had it not been for the electric chain which we had but just before got up; this carried the Lightning or Electrical matter over the side clear of the ship.”

On 25th October Cook reopened communication with the Admiralty, forwarding to Mr. Stephens, by the Dutch East Indiaman Kronenberg, Captain F. Kelgar, a packet containing a copy of his Journal (sold to Mr. John Corner in 1890), charts of the South Seas, New Zealand, and the East Coast of Australia.  He also wrote a letter giving an outline of his voyage up to date, and concludes: 

“In this Journal, I have with undisguised Truth and without gloss, inserted the whole transactions of the Voyage, and made such remarks and have given such descriptions of things as I thought was necessary, in the best manner I was capable of.  Although the discoverys made in the Voyage are not great, yet I flatter myself they are such as may merit the Attention of their Lordships, and altho’ I have failed in discovering the so much talked of Southern Continent (which perhaps do not exist), and which I myself had much at heart, yet I am confident that no part of the failure of such discovery can be laid to my charge.  Had we been so fortunate not to have run ashore, much more would have been done in the latter part of the Voyage than what was, but as it is, I presume this Voyage will be found as compleat as any before made to the South Seas on the same account.