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A treaty was negotiated for there to be a trading port on the island and that lead to making Singapore a crown colony.
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Self-Government was carried out slowly. Limited local elections started in 1948 and were fully self-governed by 1959.
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Malaysia was a merge of Malaya, Singapore, North Borneo, and Sarawak. Singapore was no longer a British Colony.
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After Singapore joined Malaysia, the Treaty was dissolved and Singapore was no longer a British Crown Colony.
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Eventually Singapore left Malaysia and became it's own independent country in Southeast Asia.