In 1990 the Greek Cypriot side unilaterally applied for membership in the EU on behalf of Cyprus as a whole. This application was made in contravention of the law and in complete disregard of the fact that since 1963 there had not been a joint government representative of the entire island. The Greek Cypriot side perceived EU membership as a way of achieving dominance on the whole of the island and ensuring a more favorable position for Greece (a member of the EU) than Turkey ( a non-member) over Cyprus. In fact, the Greek Cypriot side has never concealed that it has initiated the EU membership process to get rid of the above- mentioned internal and external balances that it felt prevented extension of Greek Cypriot control over the Turkish Cypriots. Mr. Clerides, the leader of the Greek Cypriots, saw nothing wrong in telling his people that once "Cyprus" was accepted as a member of the EU, the national cause of Hellenism would triumph as the Treaty of Guarantee would be inapplicable against a member state. He went further by stating that the principles that had so far emerged regarding a bi-zonal, bi-communal settlement would have no status or meaning under EU legislation.

From the very start, Turkey and the TRNC opposed the application made by the Greek Cypriot Administration of South Cyprus as unlawful and illegitimate. They objected on the grounds that this application was done and processed in the absence of a joint authority competent to act on behalf of the whole island. They stressed that the established parameters envisioned that EU membership could only be discussed and agreed upon after an overall settlement. Moreover, Turkey and the TRNC maintained that the 1959/1960 Agreements do not permit Cyprus to join international organizations and pacts of alliance in which both Turkey and Greece do not participate.

The period as of 1990 has been overshadowed by this application. Though fully undermining the UN negotiating process, the Greek Cypriot administration insisted on proceeding with EU membership. Finally, at the Luxembourg Summit of December 1997, the EU decided to open membership negotiations with the Greek Cypriots. The effect of this decision was two-fold. First, it marked the beginning of unilateral and illegal process of Greek Cypriot accession to the Union. Second, the parameters that had evolved for a federal settlement became invalid and inapplicable.

The destruction of the framework for a federal settlement and the relevant parameters brought Cyprus to a new phase. Looking at this situation, the Turkish Cypriots stressed that a fundamental change was required in the mentality and approach of the Greek Cypriots before a new partnership became a viable project. They maintained that the Greek Cypriots, as a first step, should acknowledge the sovereign equality of the Turkish Cypriot side. Later, in August 1998, the Turkish Cypriot side put forward the confederation proposal, which addresses all the legitimate concerns of the parties, including the status of the two sides and the Turkish-Greek balance over Cyprus. It also provides that a policy of accession can be pursued by the joint agreement of the two parties if Turkey is accorded the rights of an EU member with regard to Cyprus. The Greek Cypriot side has so far declined to negotiate on this basis.