[1][2] In 1842 Muhammad challenged the reign of his grand uncle Abdullah bin Ahmad Al Khalifa and declared himself as the ruler of Bahrain and Qatar.
[1][3] In early 1843 Muhammad returned to Qatar and then to Bahrain, and in April 1843 he defeated Abdullah bin Ahmad Al Khalifa becoming the ruler.
Faisal's inability to seize Bahrain was, in part, due to the firm stance of the British government against Saudi expansion in the Persian Gulf.
Shortly after the fighting had taken place, Mohammed bin Thani, an influential tribal leader in Al Bidda, pursued a separate peace agreement with Faisal and agreed to his governance, a move seen as a betrayal by the Bahrainis.
The blockading force, however, soon found itself engaged by a superior flotilla of 18 warships, manned by Utubi exiles from Qais Island allied with Faisal bin Turki.
[13] In the aftermath of the battle and subsequent naval skirmish, Muhammad bin Khalifa faced a complex diplomatic situation.
His brother's evacuation of the fort at Al Bidda on 8 June, 1851 marked a significant loss of Bahraini influence in Qatar.
[13] However, facing pressure from multiple sides and fearing further erosion of Bahraini influence, Muhammad bin Khalifa eventually agreed to a peace settlement.
In return, Faisal agreed to restore the fort of Al Bidda to Bahraini control and to cease interference in Qatari affairs.
[17] In addition, due to the extensive intrafamilial fractions Britain blockaded the islands of Bahrain and took all of the Al Khalifa members into custody imposing conditions that resulted in the changing the ruler.
He wrote to Isa bin Ali, promising to pay him a ransom for Muhammad's release: a thousand of the finest camels and ninety of the noblest horses.