While the outbreak of the second intifada mortally wounded the EU's vision of peace in the Middle East through regional cooperation, the events that followed definitely killed it, at least for the foreseeable future. The 2001 9/11 attacks, the 2003 invasion of Iraq, the 2004–5 terror attacks in Madrid and London, the 2006 war in Lebanon – all contributed to make the EU's vision of peace in the Middle East through regional cooperation look like a distant dream from the past decade. This development, however, did not stop the EU from continuing talking about peace in the Middle East through regional cooperation, even if it was quite clear after the 9/11 attacks that the Middle East was headed for more conflicts, rather than less. One clear result of the peace process and the period that followed 9/11 was that the EU started more and more to talk about a distinct Israeli–Palestinian conflict, rather than a wider Israeli–Arab conflict. Among other things, this meant that the Israeli–Lebanese/Hezbollah conflict and the Israeli–Syrian conflict became more and more separated from the Israeli–Palestinian track. Iran's ascending role in the Middle East also contributed to this. Another clear result of 9/11 was that a ‘war on terrorism narrative’ became much more prominent in the EU's declarations, which in turn led to more sympathy/less criticism of Israel and less sympathy/more criticism of the Palestinians during the 2000s. This culminated with the 2008–9 Gaza war, which passed without criticism of Israel in the Bulletin.

The EU's vision of a just peace in the conflict also developed during the 2000–9 period, from the second intifada to the first Gaza war. The main development was that the 2002 Seville Declaration for the first time mentioned the 1967 borders and some of the final status issues in relation to the two-state solution.