On October 25, 49 Brigade sailed into Surabaya harbour. The CO, Brigadier Mallaby, had been a major-general on Mountbatten's staff during the war, and had dropped a rank to gain experience of command. He is remembered as a humane, thinking soldier who preferred jaw-jaw to war-war. It was a battle-hardened brigade of 4,000 Indian infantry, but many of its officers, such as Mallaby, had recently arrived from staff jobs.

An initial foray by Mallaby's intrepid brigade intelligence officer, Captain Douglas MacDonald, established contact with the local commander, Moestopo, who agreed not to oppose 49 Brigade's landing. Moestopo told MacDonald that Soerio, the political leader of Surabaya, had wanted him shot and thrown into the harbour. Detachments of troops began to land and move to positions throughout Surabaya. Brigade HQ was established near the port. One memoir of this day recalls the pervasive atmosphere of menace, with armed men peering from the shadows. Around Surabaya there were in fact at least 20,000 heavily-armed and well-trained members of the TKR, the new Indonesian army, as well as at least 100,000 armed Pemuda irregulars.

A relatively amicable meeting took place on October 26 during which Mallaby assured the Indonesians that he had no Dutch with him and that his task was evacuating PoWs and the Japanese garrison. The piecemeal advance of 49 Brigade continued, closely monitored by the Indonesians. The main refugee camp at Darmo, with 6,000 Dutch and Eurasian civilians, was occupied.

Matters seemed to be proceeding reasonably well. Although suspicious, the Indonesians were not directly opposing the British. Mallaby had chosen a bold course, relying on his ability to talk his way out of trouble and the swift movement of his experienced troops through Surabaya. But he knew that they were spread out and horribly outnumbered.

Disaster struck on the morning of October 27. Unknown to Mallaby, a British plane flew over Surabaya dropping leaflets requiring all Indonesians to surrender their arms within 48 hours or be shot. The leaflets were signed by the CO of 23rd Division, General Douglas Hawthorn, safe in his Batavia HQ. Hawthorn was loathed by most of his subordinates who regarded him as over-promoted and over-fond of the good life: his ADC, Captain Dirk Bogarde, was reputed to keep him supplied with women.

Mallaby told Moestopo that he had no choice but to break his agreement and enforce what he regarded as an order. He begged for understanding but from that moment meaningful contact was lost with the Indonesians. Despite this, troops continued to land and move into the city, while civilians continued to be moved from smaller camps to Darmo.

On the afternoon of October 28, the TKR and Pemuda struck all across the city, killing 11 British officers and 44 Indian other ranks in a matter of minutes. Numerous small outposts were overrun, and a lorry convoy with hundreds of Dutch and Eurasian women and children was attacked with great loss of life. Fighting resumed at first light next morning and the situation became desperate, as many detachments were short of ammunition. Survivors recalled the attackers' reckless ferocity.

Mallaby contacted Christison, who persuaded Sukarno himself to fly to Surabaya to negotiate a ceasefire. This was only partially successful, and on October 30 Gen Hawthorn arrived to talk to Sukarno and Mallaby. It was agreed that the British would regroup and continue extracting internees, allowing the Indonesians to hold the centre of town. Whatever the terms negotiated by Sukarno, many Indonesians thought the British had surrendered. When they realised this was not so, fighting began again. Sukarno and Hawthorn had meanwhile returned to Batavia.