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Expansion in present day South Asia

The company, which benefited from the imperial patronage, soon expanded its commercial trading operations. It eclipsed the Portuguese Estado da Índia, which had established bases in Goa, Chittagong, and Bombay – Portugal later ceded Bombay to England as part of the dowry of Catherine of Braganza on her marriage to King Charles II. The East India Company also launched a joint attack with the Dutch United East India Company (VOC) on Portuguese and Spanish ships off the coast of China that helped secure EIC ports in China, independently attacking the Portuguese in the Persian Gulf Residencies primarily for political reasons. The company established trading posts in Surat (1619) and Madras (1639). By 1647, the company had 23 factories and settlements in India, and 90 employees. Many of the major factories became some of the most populated and commercially influential cities in Bengal, including the walled forts of Fort William in Bengal, Fort St George in Madras, and Bombay Castle.

The first century of the Company, despite its original profits coming primarily from piracy in the Spice Islands between competing European powers and their companies, saw the East India Company change focus after suffering a major setback in 1623 when their factory in Amboyna in the Moluccas was attacked by the Dutch. This compelled the company to formally abandon their efforts in the Spice Islands and turn their attention to Bengal where by this time they were making steady, if less exciting, profits. After gaining the indifferent patronage of the Mughal Empire, whose cities were 'the megacities of their time' and whose wealth was unrivaled outside of Asia in the 17th Century, the Company spent its first century of life in the Mughal ruled areas cultivating their relationship with the Mughal Dynasty and conducting peaceful trade at great profit. At first it should be said the EIC was drawn into the Mughal system, acting as a kind of vassal to Mughal authority in present day Bangladesh: where it was from this position that the EIC would ultimately outplay and outmaneuver everyone else in the region to eventually use that same system to hold power. What started as trading posts on undesirable land, often islands or rich fertile lands 'near' existing population centers were developed into sprawling factory complexes with hundreds of workers providing exotic goods back to England and offered protected points to export English finished goods to local merchants. The Company's initial rise in Bengal and successes generally came at the expense of competing European powers through the art of currying favors and well placed bribes as the company was matched at every step with French expansion in the region (whose equivalent company carried substantial royal support). See French East India Company. Throughout the entire century the company only resorted to force against the Mughals once, with terrible consequences. The Anglo-Mughal war (1686–1690) was a complete loss, ending when the EIC effectively declared fealty to the Mughals to get their factories back.

The East India Company's fortunes changed for the better in 1707 as Bengal and other regions under Mughal rule fell into Anarchy with the death of the Mughal Emperor Aurangzeb. A series of large scale rebellions and the collapse of the Mughal taxation system led to the effective independence of virtually all of the Mughal's pre-1707 fiefs and holdings, with their capital Delhi routinely under the control of either Maratha, Afghan or usurper General's armies. The EIC was able to take advantage of this chaos, slowly wresting direct control of the province of Bengal and fought numerous wars with the French in the Carnatic wars for influence and control of the east coast. The Company's position in the Mughal court as it fell apart made it possible to sponsor different players on the continent as they individually contended with others, steadily amassing an ever larger position on the continent for themselves.

In the 18th Century, the primary tool of the Company's profits in Bengal became taxation in conquered and controlled provinces, as the factories became fortresses and administrative hubs for networks of tax collectors that expanded into enormous cities. The Mughal Empire was the richest in the world in 1700, and the East India Company tried to strip it bare for a century thereafter. Dalrymple calls it "the single largest transfer of wealth until the Nazis." What was in the 17th century the production capital of the world for textiles was forced to become a market for British made textiles. Mansions of statues and their jewels, untold material wealth, was moved from the palaces of Bengal to the townhouses of the English countryside. Bengal in particular suffered the worst of Company tax farming, highlighted by the Great Bengal famine of 1770, which even inspired a reprisal from the King in response to the brutality. Meanwhile, the primary tool of expansion for the company was the Sepoy. The Sepoy was a locally raised, mostly Muslim, western trained and equipped soldiers that changed warfare in present day South Asia. Mounted forces and their superior mobility had been king on the regions battlefields for a thousand years, cannon so well integrated the Mughals fought with cannon mounted on elephants: all were little match to line infantry with decent discipline supported with field cannon. A few thousand company sepoys, time and again, took on vastly superior Mughal forces numerically and came out victorious; sieged fortifications. Often despite poor command to the point that the Afghan, Mughal and Maratha forces started building and supporting their own western style forces, often French equipped, as the chaos widened and the stakes were raised to varying success. In the end the company won out, generally through as much diplomacy and state-craft(fraud and deception). The gradual rise of the EIC within the Mughal network culminated in the Second Anglo-Maratha War, where the Company successfully ousted the Empire's official protectors in the Maratha, the Maratha high water point in their rise to power, and installed a young Mughal Prince as Emperor with the Company as the de jure protectors of the Empire from their position of direct control in Bengal. This relationship was repeatedly strained as the Company continued its expansion and exploitation, however it lasted in some form until 1858 when the last Mughal Emperor was exiled as the Company was disbanded and its assets were taken over by the British Crown.

In 1634, the Mughal emperor Shah Jahan extended his hospitality to the English traders to the richest region of the Mutual Empire Bengal, and in 1717 customs duties were completely waived for the English in Bengal. The company's mainstay businesses were by then cotton, silk, opium, indigo dye, saltpetre, and tea. The Dutch were aggressive competitors and had meanwhile expanded their monopoly of the spice trade in the Straits of Malacca by ousting the Portuguese in 1640–1641. With reduced Portuguese and Spanish influence in the region, the EIC and VOC entered a period of intense competition, resulting in the Anglo-Dutch wars of the 17th and 18th centuries. The British were also interested in trans-Himalayan trade routes, as they would create access to untapped markets for British manufactured goods in Tibet and China. This economic interest was showcased by the Anglo-Nepalese war (1814–1816).