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Dr. H.A. Hellyer, writing from Cairo, is an associate fellow of the Royal United Services Institute in London and the Brookings Institution in Washington. He is on Twitter at @hahellyer.

Egypt's judicial system has, once again, shocked the international community. The death sentences that were recommended last month for more than 528 people – ostensibly Muslim Brotherhood supporters – seemed to be startling enough. And then, on Tuesday, a court recommended death sentences for 683 people, including the supreme guide of the Muslim Brotherhood, Mohammad Badie.

What quite happened? What are the prospects for these cases, and what are the larger implications of them?

The Minya Criminal Court heard the first case, popularly referred to as the 'Minya 528' trial, last month. Its recommendation was condemned by a number of political figures inside and outside of Egypt, including many who support the military-backed interim government.

The court was presided by a three-judge panel, with a death sentence recommended for the 528 defendants. The head judge has a reputation for some notoriety already, to put it mildly. Popular sentiment hints that the defendants are all Brotherhood supporters, while there is substantial evidence from press interviews with family members to suggest that many of these defendants have no such affiliation. Not that it would make the trial's results any less disturbing if they did – the entire proceedings did not exceed more than a few hours in total, and legal experts as well as human-rights groups were rightfully livid about the process.

Most of these defendants were tried in absentia. This, in turn, triggers a certain procedural process. According to legal experts, Egyptian law does not allow absentee defendants to present a defense in front of the court. It is usual that those in absentia receive, therefore, a rather harsh sentence, but it is not obligatory for them to receive the highest penalty. In this case, they did receive such a penalty in the recommended sentence, and then tremendously harsh sentences in the actual verdict. In either case, they automatically get a retrial. Whether the defendants are absentee ones or not, legal experts find it difficult to imagine that the Court of Cassation, which is due to hear the case next, will not overturn the sentences. That, obviously, does not obviate the seriousness of what this all implies.

After the court recommended the death sentence, the recommendation was sent to the office of the Grand Mufti of Egypt. The Grand Mufti is formally a part of the Ministry of Justice and is considered on the level of minister, but his ruling is not binding. The court is free to ignore his ruling, or accept it. The Grand Mufti's office confirmed in a press release that on Sunday, April 27, he issued his confidential recommendation to the court. In the same confirmation, his office denies all press reports alluding to the contents of that recommendation.

While it would be extraordinary for the Grand Mufti to formally come out and say he disagreed with the ruling of the court, owing to his position within the Ministry of Justice, it is reasonable to draw an inference from his denial of all press reports – given that those reports had indicated that he did agree with the death sentence. We may never receive a public confirmation, but all the evidence hints that he rejected the sentences.

On Monday, the Criminal Court then issued an actual ruling, as opposed to a recommendation, which sentenced 37 people from the 528 to death, and issued a number of lesser, but still harsh, sentences for the rest.

It should be noted that none of this constitutes an appeal process. The next stage for the case is the Court of Cassation. Following this, an appeal may take place.

In addition to the above court case, another was heard on Tuesday. The same criminal court in Minya recommended that 683 people be sentenced to death. The recommendation will be sent to the Grand Mufti's office for consultation before a ruling on the death sentence is actually issued by the criminal court.

Again, legal experts find it dubious that the Court of Cassation will not overturn such rulings. This, however, does not mean the decisions are meaningless. Indeed, they have already had a substantial and destructive effect, not least upon the defendants and their families. Additionally, the international repercussions to Egypt's standing should not be underestimated – on Tuesday, perhaps in part due to the trial's conclusions, U.S. Senator Patrick Leahy, chair of the Senatee's State Department and Foreign Operations panel, put the brakes on releasing military aid to Egypt.

The suggestion has been made that these sentences and recommendations were the collective result of some sort of direction from more senior figures within the Egyptian state. This remains somewhat dubious. If anything, the judiciary's actions in this regard are making things more, not less, difficult for the Egyptian state – both domestically as well as internationally, with the United Nations Secretary General indicating he will raise the issue in person with the Egyptian Foreign Minister later this week.

However, it is also of note that no senior public official of the Egyptian has condemned the rulings. Political figures and parties have taken such a stance across the Egyptian spectrum, with the strongest criticism coming from Non-Governmental Organizations such as the Egyptian Initiative for Personal Rights and the Cairo Institute for Human Rights.

As yet, however, no official organ of the state itself has issued any sort of statement criticizing the ruling for being draconian. The Prosecutor General himself has indicated a desire for an appeal, but no senior official in government has, as yet, come out against the verdicts. Will they do so once the court cases have run their courses? Or is it, as many suggest, the case that parts of the Egyptian state are not simply independent, but essentially autonomous beyond ordinary notions of unitary state control?

Egyptians, and many others, wait to see. In the meantime, Egypt's transition will continue to flummox – as well astonish – many inside and outside of Egypt.