He controlled the settlement which was located almost straight across the Johor River from the royal administrative center and capital Batu Sawar.
His half-brother Alauddin Riayat Shah III who had fallen from power at the time of Iskandar Muda's offensive on Johor in 1613 had fled to Lingga and probably died there in or around 1615.
In 1618, Abdullah Ma'ayat Shah moved to Lingga and gained the support of Orang Laut and the Dutch to wage a war against Aceh.
Abdul Jalil Shah was then put on the throne of Pahang by the Laksamana, but only under the condition that Raja Bajau succeed him when he reached his majority.
[3] In 1603 Raja Bongsu was instrumental in forging early diplomatic relations with the Dutch by lending assistance to Admiral Jacob van Heemskerck on 25 February 1603 in attacking and plundering the Portuguese carrack Santa Catarina, in the Johor River estuary off present-day Singapore.
Megat Mansur did not survive the voyage, but other members of the Johor embassy did and returned with the fleet under the command of Admiral Cornelis Matelief de Jonge in 1606.