On 1 November 1999 de Soto was selected as the Secretary-General's Special Adviser on Cyprus, with the rank of Under-Secretary-General; he held this post until the dismantling of the Special Mission to Cyprus following the April 2004 rejection of the Annan Plan for a Cypriot bizonal bicommunal federation divided along ethnic and religious lines.
Under the terms of the Annan Plan for Cyprus, a United Nations proposal to settle the Cyprus dispute, a new national flag would have been adopted by a reconstituted confederal republic of Cyprus.
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