At the end of last week, Egyptian military chief Field Marshall Abdel Fattah el-Sisi announced that he would be resigning his military post to run for this year's presidential elections, expected to take place in May. It is a move that has been mooted for months now, and has at its origins the military's ouster of the Egypt's first democratically elected president, Mohammed Morsi of the Muslim Brotherhood, last June.

Everyone expects Sisi to win. He is genuinely popular among older Egyptians who want a strong hand to restore stability. The opposition, both Islamist and secular, has been corralled – in large part as a result of the extensive military crackdown that has seen large numbers arrested, especially from the now banned Muslim Brotherhood.

Sisi will also have strong backing from outside the country. Israel is certainly happier that the military is back in charge after the brief reign of the Muslim Brotherhood. Saudi Arabia and the UAE have been pouring money into Egypt in support of the military since last year's coup.

I fear, however, that a Sisi presidency is not going to return stability to Egypt in the short-to-medium term. As I note in Next-Gen Jihad in the Middle East, published today, this has major implications for the region and even for Australia.

A return to authoritarianism may provide a short-term balm for those who feared the ascent of Islamists over the last three years. But as history has shown repeatedly, authoritarianism in the Middle East has also been a great incubator and amplifier for extremist ideas and activism.

As I explain in my paper, at the heart of the problem in Egypt is the conflict between the military and the Brotherhood.

The military and the security services – or at least the most hard-line elements in each – seem to genuinely believe they can wipe the Brotherhood out. The Brotherhood, on the other hand, is more than happy to play the role of martyr to win back public support after its brief and incompetent rule.

But neither of these things is going to happen any time soon. And until Egypt's most important national institution reaches an accommodation with its largest opposition movement, there will violence, instability and radicalisation.

There are two main dangers. First, that the conflict will radicalise elements of the Brotherhood and other young Egyptians unhappy with the military crackdown. Some in the Brotherhood are already debating the wisdom of sticking to a non-violent approach to politics.

Second, that the turmoil will be exploited by more extreme jihadist groups which are already fighting a serious insurgency in the Sinai and since the coup have been mounting more attacks in the rest of Egypt.

It may well be that the military will prevail eventually. But it took the Mubarak regime almost a decade in the 1990s to tackle a major challenge from Islamist groups that saw, among other things, terrorist attacks against foreign tourists, the mainstay of the Egyptian economy. That regime was more coherent and stronger than the current one. But most importantly, that regime was not facing the economic situation Egypt faces today, with a collapse in tourism and foreign investment (real foreign investment, not just Gulf largesse).

All of this should concern countries outside the region. The regional tumult from Syria to Libya has already created fertile ground for jihadist groups. The immediate concern is obviously with those foreigners – including Australians – travelling to Syria, where they are gaining combat experience and military skills, and can form new connections with extremist groups from around the world.

An extended period of unrest in Egypt will add to the regional turmoil and swell extremist numbers in the region even further. Given Egypt's historic role as a centre of Islamist thinking, the conflict there will throw up new leaders as well. And while it is true that the current focus of jihadist groups is on the Middle East, recent history teaches us that this can shift quickly. Most of al Qaeda's leaders were veterans of domestic conflicts in the region in the 1980s and 90s.

Of course, there is nothing inevitable about the trajectory of events in Egypt. It may be that once Sisi wins the presidential elections and after any subsequent parliamentary elections, the military will feel confident enough to seek an accommodation with the Brotherhood and pull back from its crackdown on political dissent. But at this stage, the polarised and uncompromising atmosphere does not make this seem likely.

Photo by Flickr user Zoriah.