The first important fact in the history of the Expedition was the discovery of the advantage of the Kongone entrance of the Zambesi, the best of all the mouths of the river for navigation. Soon after a site was fixed on as a depôt, and while the luggage and stores were being landed at it, there occurred an unfortunate collision with the naval officer, who tendered his resignation. At first Livingstone declined to accept of it, but on its being tendered a second time he allowed the officer to go. It vexed him to the last degree to have this difference so early, nor did he part with the officer without much forbearance and anxiety to ward off the breach. In his despatches to Government the whole circumstances were fully detailed. Letters to Mr. Maclear and other private friends give a still more detailed narrative. In a few quarters blame was cast upon him, and in the Cape newspapers the affair was much commented on. In due time there came a reply from Lord Malmesbury, then Foreign Secretary, dated 26th April, 1859, to the effect that after full inquiry by himself, and after consulting with the Admiralty, his opinion was that the officer had failed to clear himself, and that Dr. Livingstone's proceedings were fully approved. Livingstone had received authority to stop the pay of any member of the Expedition that should prove unsatisfactory; this, of course, subjected his conduct to the severer criticism.
When the officer left, Livingstone calmly took his place, adding the charge of the ship to his other duties. This step would appear alike rash and presumptuous, did we not know that he never undertook any work without full deliberation, and did we not remember that in the course of three sea-voyages which he had performed he had had opportunities of seeing how a ship was managed--opportunities of which, no doubt, with his great activity of mind, he had availed himself most thoroughly. The facility with which he could assume a new function, and do its duties as if he had been accustomed to it all his life, was one of the most remarkable things about him. His chief regret in taking the new burden was, that it would limit his intercourse with the natives, and prevent him from doing as much missionary work as he desired. Writing soon after to Miss Whately, of Dublin, he says: "It was imagined we could not help ourselves, but I took the task of navigating on myself, and have conducted the steamer over 1600 miles, though as far as my likings go, I would as soon drive a cab in November fogs in London as be 'skipper' in this hot sun; but I shall go through with it as a duty." To his friend Mr. Young he makes humorous reference to his awkwardness in nautical language: "My great difficulty is calling out 'starboard' when I mean 'port,' and feeling crusty when I see the helmsman putting the helm the wrong way."
Another difficulty arose from the state of the country north of the Zambesi, in consequence of the natives having rebelled against the Portuguese and being in a state of war. Livingstone was cautioned that he would be attacked if he ventured to penetrate into the country. He resolved to keep out of the quarrel, but to push on in spite of it. At one time his party, being mistaken for Portuguese, were on the point of being fired on, but on Livingstone shouting out that they were English the natives let them alone. On reaching Tette he found his old followers in ecstasies at seeing him; the Portuguese Government had done nothing for them, but Major Sicard, the excellent Governor of Tette, had helped them to find employment and maintain themselves. Thirty had died of small-pox; six had been killed by an unfriendly chief. When the survivors saw Dr. Livingstone, they said: "The Tette people often taunted us by saying, 'Your Englishman will never return;' but we trusted you, and now we shall sleep." It gave Livingstone a new hold on them and on the natives generally, that he had proved true to his promise, and had come back as he had said. As the men had found ways of living at Tette, Livingstone was not obliged to take them to their home immediately.