Clifford arrived in Malaya in 1883 aged seventeen. The British then administered the colony of the Straits Settlements while in the west coast Malay states residents were establishing an 'advisory system' to disguise British control under a cloak of Malay sovereignty. Clifford's first posting outside Singapore was as secretary to Hugh Low, the venerable resident of Perak. In 1887 Weld dispatched Clifford on a mission to the east coast state of Pahang, where he successfully persuaded its ruler to accept British control of external affairs. Clifford was then appointed British agent in Pahang, but his powers were limited and within a year Sir Cecil Clementi-Smith, Weld's successor as governor, compelled the sultan to upgrade the British agent to resident. A senior official, John Rodger, was appointed to this position while Clifford sailed to England with acute dysentery. He returned in 1890 as superintendent of Ulu Pahang (the interior), where between 1891 and 1895 he led the suppression of armed resistance. Once this was settled, Clifford was advanced to resident of Pahang, which in 1896 became part of the Federated Malay States. For Clifford adventure gave way to administration as he moved from the frontier to the secretariat. In 1900 he was seconded to the British North Borneo Company and served as governor of North Borneo until a dispute with the directors led to his resignation.
His first novel, Since the Beginning, came out in 1898. Thus, when ill health obliged him to write for a living, he was building on an established reputation and within a literary circle which included Joseph Conrad. His stories cover the poignant interaction of Europe and Asia, illustrated by the predicament of the political officer alone in an alien and potentially hostile environment or the fatal impact of modernization upon Malays. For example, Saleh, the eponymous hero of two novels, is educated in England but rejected by the English when he woos his host's daughter. On his return to his father's court he dies while leading an armed rising. In the foreword to Saleh: a Sequel Clifford spells out the dangers of the British 'endeavouring to impose on their Oriental brethren education of a purely Occidental type', which the fictional British officer endorses with the lament: 'May God forgive us for our sorry deeds and for our glorious intentions!'
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