After the fall of Melaka to the Portuguese, Sultan Mahmud of Melaka and his eldest son, Ahmad, took refuge in the hinterland, hoping that the Portuguese invaders would, after plundering the town, return to their colonial base in Goa, India - as was the custom in wars of the time. Much to his dismay, the Portuguese not only stayed but also set upon the tremendous task of building an impregnable fort overlooking the town. This clearly stated their intention to remain permanently in Melaka and their determination to resist any attempt by the defeated Sultan to re-capture his capital. Six months after the capture of Melaka, the stone fortress, 'A Famosa', was ready. The Portuguese were permanently established as the supreme military, naval and trading power on the Straits, in place of the old Melaka sultanate.

In the meantime, Sultan Mahmud and his son built stockades in the hinterland of Melaka for carrying out raids on the Portuguese fortress in Melaka. Overland raids were carried out from Pagoh, in Ulu Muar, while sea raids were launched from the stockade in Bentayan at the mouth of the Muar River. For over a period of time, intermittent raids were carried out both by land and sea caused considerable hardship for the Portuguese at Melaka. There were times when the Portuguese wanted to give up the idea of staying on in Melaka and return to Goa. But eventually, fresh reinforcements arrived and the Portuguese counter-attacked, destroying the Malay strongholds of Pagoh and Bentayan. Sultan Mahmud and his followers withdrew further inland through Ulu Jempol to Pahang. After about a year in Pahang, Sultan Mahmud and his family sailed to Bentan where he established a new capital.

The defeat of the Royal House of Melaka aroused not only the loyal Malay followers of the ex-Sultan Mahmud. There was still a considerable number of Javanese and they detested the policy of the Portuguese government to monopolise trade and spread Christianity among the inhabitants. One revolt was organised by a Javanese named Patih Kadir, but the Portuguese succeeded in crushing it. Later, a strong force of Javanese soldiers under the leadership of Patih Yunus, prince of the Muslim state of Demak, besieged Melaka. But the fortress repelled all attacks and the invaders retreated with the arrival of reinforcements from Goa.

Sultan Mahmud continued his attacks from Bentan, organising hit-and-run raids on the fort in Melaka, blockading the port and plundering Portuguese ships in the Straits. These raids and blockades were, to a certain extent, quite effective. In 1524, for instance, the price of commodities in Melaka was more than doubled. But the town remained in Portuguese hands.

The fall of the Melaka Sultanate also had repercussions on the Malay states on the Sumatran coast across the Straits of Melaka. The states particularly affected were those which had been subject to Melaka, such as Lingga, Siak, Indragiri and Aru, now the present state of Deli. The princes of these states with their followers went to Sultan Mahmud at Bentan with a view to helping him re-capture Melaka.

However, Raja Abdullah, a nephew of Sultan Mahmud, and the Raja of Kampar went over to the Portuguese side and was made a Bendahara of Melaka by them. Not long after, the Portuguese themselves turned on the traitor and he was executed in a public market.

Seeing that the Malays under Sultan Mahmud were gathering forces in Bentan, the Portuguese made several attempts to invade and destroy the stronghold. But the Malays threw back the attacks and the Portuguese suffered heavy losses. Finally in 1526, a larger force of Portuguese ships under the command of Pedro Mascarenhaas was sent to Bentan, and this time, the Portuguese managed to burn and plunder the towns of Kopak and Kota Kara. Sultan Mahmud and his family fled across the Straits to Kampar in Sumatra, where he died two years later.

After his death, his son, Raja Mudzafar, made his way up to Perak where he founded the dynasty of Malay sultans who still reign there today. In 1520, another son of Sultan Mahmud, Ala'uddin, made his capital on the Johor River and became the first Sultan of Johor - founding the Johor Empire.

In the meantime, attacks on the Portuguese in Melaka continued. The two sons of Sultan Mahmud made periodical raids from Johor and Perak, and they were helped by the Sultan of Pahang. There were also raids from Siak and by a Javanese prince from Japara. But most of the raids were disorganised attacks by small bands of Malays, and the Portuguese maintained supremacy behind their impregnable 'A Famosa'. The Johor rulers continued preying on Portuguese merchant vessels, and the Portuguese retaliated by sending punitive expeditions.

At about the same time a new power was rising among the Malay states - the Kingdom of Aceh, which had long been a strongly Muslim State. The Achinese crossed the Straits of Melaka in great numbers to carry out raids on their trading rival, Melaka. For the Achinese, the wars against Melaka were also part of a policy of expansion into the Malay Peninsula - they not only attacked Melaka but also raided Johor, Pahang, Perak and Kedah. Ironically, it was this Achinese threat that made the Portuguese and the Johor Malays frequently enjoy periods of truce, and even to ally themselves and co-operate with one another against a common enemy. This disunity among the Malay powers resulted in a further prolonging of the supremacy of the Portuguese.

Johor entered into a ruinous war with the Sumatran state of Jambi in 1666, a war which ended in the destruction of the Johor capital at Batu Sawar in 1673. Court intrigues, and disputes over succession to the throne undermined the vitality of Johor. In the eighteenth century, Johor became an easy prey to Bugis infiltration.

For long periods, the Portuguese in Melaka were on the defensive: politically isolated, and numerically inferior to their enemies. During their rule, Melaka became the most fought-over piece of territory in Asia - bombarded, besieged, blockaded, attacked dozens of times by almost every major power in the Archipelago.

But despite such strong handicaps, they successfully fought off every Malay attack on Melaka. The Malay powers failed because they were unable to form a united front against the Portuguese. Disunity rather than unity was the feature of Malay politics in the sixteenth century, and the presence of a common enemy was at that time not sufficient to bring about some form of coalition. Malay states were even at times briefly allied the infidel Portuguese in their wars against other Malay states.

It was left to another European power to organise this coalition and to finally overthrow Portuguese power in Melaka. .

The rise and fall of a crusading nation