Europe should remember that the elements in Egypt that are now likely to be on top of the political system - the Army, the judiciary, the intelligence services -  represent a completely unreformed inheritance from the “deep state” as it existed under Mubarak.  

The killing of at least 51 Muslim Brotherhood supporters by the Egyptian army early on Monday morning marks a disturbing escalation in the confrontation between Egypt’s new rulers and supporters of the deposed president, Mohamed Morsi. The events seem to fit a worrying pattern: since the army launched a coup against President Morsi last week, Egypt has seen a spiraling campaign of repression against the Muslim Brotherhood. They also show how implausible it is to think that the military’s seizure of control in Egypt is likely to advance the cause of democracy and pluralism in the country.

It remains unclear how the latest deadly confrontation unfolded, but there are credible reports that the army may have fired on unarmed demonstrators. At the least it seems to have used excessive and disproportionate force. Apart from the shootings of 8th July, the new authorities have taken a number of steps that look like a campaign of retribution against the deposed presidents’ supporters. Morsi and several other senior figures in the Brotherhood and its political wing, the Freedom and Justice Party, have been arrested or detained. Several are now the subject of police investigations. A number of Muslim Brotherhood TV stations have been taken off air, and its headquarters in Cairo sealed off. The offices of Al-Jazeera, seen as sympathetic to the Brotherhood, have been raided.

The army – standing behind the head of state it has installed, an unelected judge appointed to office by President Mubarak – now holds unchecked power. Egypt’s democratically approved constitution has been suspended in favour of a constitutional declaration issued by the country’s unaccountable leader. Liberals and opposition supporters who cheered the army’s takeover hoped to restart the revolution, but so far what is unfolding looks much more like business as usual for Mubarak’s deep state, including an attempt to rewrite history by absolving security forces of any responsibility for violence in the two and a half years since the uprising – and the apparent launching of politically-motivated prosecutions against their opponents.

The constitutional declaration issued on Monday night does not dispel these concerns. Last year’s constitution will be amended by a ten-member committee formed of six judges nominated by country’s courts and four academic experts (presumably nominated by the presidency), then reviewed by an assembly representing different social groups (without any formal power to amend the draft) and put to a referendum. It is hard to believe that this process – in which the army and judiciary have the dominant role – will repair the most serious flaws of the previous document, which consisted in expansive military power and excessive centralization. Moreover it can hardly be described as democratically accountable. After the referendum, there will be parliamentary elections within two weeks, followed by presidential elections a few months later.

Assuming this timetable holds – which surely must be open to question – the duration of the current military-backed and unaccountable regime will be limited. But a larger question surrounds the ability or desire of the country’s new authorities to bring the Muslim Brotherhood and its supporters back into the political process. While President Morsi did a poor job of trying to build political consensus for Egypt’s fledgling democracy, it will only be harder to build it now. The Brotherhood have every reason to feel that the victories they obtained in each of the five nationwide elections held since Mubarak’s fall have simply been overturned by unreformed groups that were always opposed to Islamists holding power. There had been a massive withdrawal of public support from Morsi’s regime – but Brotherhood supporters are entitled to feel there is much less legitimacy in a new political order imposed at the point of a gun. And instead of acting to reassure Morsi’s followers that they have a major place in the new order, the new authorities seem to be doing everything to marginalize and exclude them. The Muslim Brotherhood, with plausible reasons to fear the return of the political suppression it suffered for so long, seems to be digging in for a campaign of all-out resistance to Morsi’s deposition, epitomized by its call for supporters to rise up.

The implications of these developments for Egypt’s political development and the wider struggle for democracy and pluralism in the Arab world are potentially enormous. The obvious danger is that Islamic political movements will draw the conclusion that their participation in democratic politics is a wasted effort. Europe needs to react to this complicated and fraught situation with care but also with clarity, in a way that will best serve the values and interests it has at a pivotal moment in the region. Initial responses from European leaders have suggested uncertainty over what line to take, with several officials opting for a cautious approach to the army’s actions. Official statements from EU High Representative Catherine Ashton have avoided any condemnation of the military seizure of power (though she did in her most recent statement stress the responsibility of the interim authorities to pursue reconciliation). There is often a difficult balance to strike between private dialogue and public criticism – but European officials must take care to avoid seeming to downplay actions that violate core democratic principles and human rights.

The first priority must be to try to avoid further violence at a moment of high tension and danger. The army and interim leadership must clearly end their crackdown against the Muslim Brotherhood and ensure there is a credible and independent investigation into the shootings of 8th July. In the current polarised environment, Morsi’s supporters will be sceptical of any process set up by the new authorities – and the onus must be on the army and interim president to demonstrate that the investigation will be impartial and open. It is essential that the army and security forces avoid any further excessive use of force or other repressive acts. The EU should press for the release of leading figures from the Brotherhood and the Freedom and Justice Party who have been arrested. MB television channels should also be restored to air. EU officials should press for access to Morsi and other MB leaders. At the same time, the Brotherhood should be encouraged to make clear that all protests by their supporters must remain non-violent.

The emphasis of the EU should be on constructive actions that can help reduce the risk of confrontation and try to steer Egypt back towards inclusive dialogue. At the same time, Europeans must remember that a significant body of opinion in Egypt (essentially, the Muslim Brotherhood’s supporters) has every reason to reject the legitimacy of the new “road map.” European statements should be sensitive to the need not to endorse the new timetable for elections, but rather to emphasise the fundamental principles of democratically accountable and limited government under the rule of law. I have argued in previous publications that military coups against elected leaders are a “red line” that should trigger a slow-down in engagement under the EU’s new neighbourhood policy. While the complexity of the current Egyptian situation argues against suspending all aid and cooperation programs at this point, the EU should keep a close watch on the evolving transition back to democratic rule and make clear if necessary that it is prepared to cut back on its engagement if the country is not on a democratic path. The EU should maintain channels with all political forces, and European officials including EUSR Bernardino Leon should engage actively to try to identify whatever scope exists for an inclusive and consensual way forward.

The EU should also remember that the elements in Egypt that are now likely to be on top of the political system – the Army, the judiciary, the intelligence services – represent a completely unreformed inheritance from the "deep state” as it existed under Mubarak. There must be a strong probability that the ultimate winner of presidential elections, if they take place in line with the new timetable, will be a political figure with links to the old regime. One of the missed opportunities of the last year was the failure of Morsi’s government to pursue any kind of institutional reform – it was too weak to do so. But there is now a serious danger that these bodies will have the political upper hand and will be confirmed in their resistance to change. The EU should therefore include in its messages in the coming period that credible reform of the security sector and the judiciary will be essential if Egypt is to find its way back to a political system based on accountability and the rule of law.

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Read more on: The Middle East and North Africa, North Africa, Egypt

The European Council on Foreign Relations does not take collective positions. This commentary, like all publications of the European Council on Foreign Relations, represents only the views of its authors.