[3][5] With a base established, the sultan rallied the disarrayed Malay forces and organised several attacks and blockades against the Portuguese position.

[6] Although Alauddin Riayat Shah II and his successor had to contend with attacks by the Portuguese in Malacca and by the Acehnese in Sumatra, they managed to maintain their hold on the Johor Sultanate.

[7] Alauddin Riayat Shah II established a new capital by the Johor River and from there continued to harass the Portuguese.

He consistently worked together with his brother in Perak and the Sultan of Pahang to retake Malacca, which by this time was protected by the fort A Famosa.

Around the same time, the Aceh Sultanate in northern Sumatra was beginning to gain substantial influence over the Strait of Malacca.

With the Portuguese and Johor frequently in conflict, Aceh launched multiple raids against both sides to tighten its grip over the strait.

[9][10] Johor later grew stronger and formed an alliance with the Dutch to attack Portuguese Malacca and conquered it on January 14, 1641, ending the triangular war.

Two treaties were signed by Admiral Cornelis Matelief de Jonge on behalf of the Dutch Estates General and Raja Bongsu (later to be Sultan Abdullah Ma'ayat Shah) of Johor in May and September 1606.

[14] Johor won the war in 1679, but in a weakened position as the Bugis refused to go home, and the Minangkabaus of Sumatra had started to assert their influence.

[15] After the sacking of Batu Sawar in 1673, the capital of Johor was frequently moved to avoid the threat of attack from Jambi.

Johor Lama (Kota Batu) was initially founded by Alauddin Riayat Shah II but was sacked by the Acehnese in 1564.

This is followed by a period with no fixed capital (places included Tanah Puteh and Makam Tauhid) during the reign of Sultan Abdul Jalil Shah III before he moved it to Batu Sawar in 1640.

Many orthodox scholars from the Indian Subcontinent and Arabia were housed in special religious hostels, while devotees of Sufism could seek initiation into one of the many Tariqah (Sufi Brotherhood) which flourished in Riau.

[20][21] Sultan Mahmud II ordered the pregnant wife of a noble, Orang Kaya Megat Sri Rama killed, as she had taken a slice of the royal jackfruit.

Both the Bugis and the Minangkabau realised that the death of Sultan Mahmud II had provided them with the chance to exert power in Johor.

[24] Throughout the latter reign of Sultan Sulaiman Badrul Alam Shah in the mid-18th century, real power was held by the Bugis.

The death of Sultan Sulaiman triggered a succession dispute, which was lost by the combined Bendahara-Temenggong court elite to the Bugis faction.

However, by the late 18th century, Engku Muda of the Temenggong faction under Sultan Mahmud Shah III gained power at the expense of the Bugis.

He was appointed by the Yam Tuan Muda of Riau, Raja Jaafar because according to him, in a Malay tradition, a person has to be by the dying sultan's side to be considered as the new ruler.

With Temenggong Abdul Rahman's help, Raffles managed to smuggle Hussein, then living in exile on one of the Riau Islands, back into Singapore.

However, Bendehara Ali claimed that he had no connection to the events in Singapore, as it is the Temenggong's fief and stated that his loyalty lies only with the Sultan of Johor in Lingga.

[32] Sultan Abdul Rahman, who had devoted himself to religion, became contented with his political sphere of influence in Lingga, where his family continued to maintain his household under the administrative direction of Raja Ja'afar who ruled under the auspices of the Dutch.

When Raja Jaffar, Yam Tuan Muda of Riau, died and Muhammad Shah was in no hurry to appoint a successor.

The sultan saw the damage that was done to the palace during his father's reign and decided to reemphasis and restore adat[33] as a rule governing personal behaviour and politics.

Conditions imposed during the appointment included paying a visit of fealty to the ruling Sultan Mahmud Muzaffar in Lingga.

Sultan Hussein of Singapore died in 1835 and his prince Tengku Ali wished for the legitimacy granted to Temenggong Ibrahim, by the British and some Malay nobles.

Worried by the state of affairs, the British called Tengku Ali back to Singapore on the threat of cancelling his pension.

[37][38] In his reply, the Bendahara reiterated that the Temenggong was supposed to swear fealty to his majesty and on the behaviour of Tengku Ali, the Bendehara claimed ignorance.

It erupted into an open dispute between Sultan Mahmud Muzaffar and the Bugis nobility over the appointment of new Yam Tuan Muda of Riau.

The Johor Sultanate established a series of shifting capitals as it navigated conflict and the changing political landscape.