While Baudin had been pushing into winter on the south coast, his second captain was turning in to Port Jackson – the British flag raised on the foremast of the Naturaliste. In hurried journal entries Emmanuel Hamelin and his officers recorded their arrival, noting the heavy rain and rough seas that signalled an incoming storm and that even upturned their dinghy and its crew in the harbour. The unfortunate men were left ashore for days, where they were cared for by a group of unnamed Aborigines, but the voyagers’ thoughts were less on their stranded companions or those men's rescuers than they were on their British hosts. Hamelin's men had caught the distant sound of music and a nine-canon salute: the colonists in Sydney Town were celebrating St George's Day and anticipating the arrival of the French voyagers – the pilot, as he guided the Naturaliste into the harbour, told Hamelin they had been hoping to see the expedition for the past year. Still, both voyagers and colonists were unaware that the Revolutionary Wars had been brought to an end by the Treaty of Amiens and so the Naturaliste was anchored, for the time being, just a short distance into the harbour at rugged Middle Head. It was from there that the first official contact between the expedition and the colony was made, as, with a cautious hand, Hamelin penned his first letter to Governor Philip Gidley King.

The Naturaliste would remain at Port Jackson three weeks before again setting sail, ostensibly, to rejoin the Géographe. But it was on its return to the British colony another three weeks later, having run short of provisions, that the expedition was reunited and under Baudin's command awaited summer. The scientific staff and their collections escaped the confines of each ship and spilled ashore, the naval staff adjusted to new routines and relationships, the commander turned to colonial politics and preparations for a new campaign.