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Thomas Tugendhat is the author of The Fog of Law, published by Policy Exchange. He was previously Military Assistant to the Chief of the Defence Staff.

As the provisional results suggest, Gen Abdul Fattah al-Sisi will be elected President of Egypt. First by force and then through the judiciary, Sisi has neutered his principal rivals – the Muslim Brotherhood. While they won the vote in 2012, this time they weren’t even be on the ballot paper.

But if the Army thinks the election will mark their victory, they’re wrong. It will only cap the Brotherhood’s defeat. Former president Mohammed Morsi’s followers are no longer the threat they once were, but this isn’t a good thing for the Army, instead it makes the real enemy harder to stop.

Since their abortive and disastrous rule, the Brotherhood’s support base has collapsed and its social networks are eroding. They are a shadow of their former selves even before any votes are left uncounted. They have been replaced by something much worse – Salafism and chaos.

For decades the Brotherhood relied on two sources of funding to provide schools and clinics and buy support: one a form of voluntary taxation from all party members, the other from wealthy expats in the Gulf. For years their different interests never clashed. After all, the leaders never had the power to deliver anything but small local projects.

But just like the Liberal Democrats, a brief spell in office is all that was needed to fracture the alliance. It was never going to survive. One side wanted protection for small businesses against the over-powerful state industries; the other wanted to replace the state monopolies with their own. The two could never be satisfied.

So today the clinics and classrooms the Muslim Brotherhood backed are running out of funds and the social support is being exhausted. Combined with the poor government, this has seen confidence in the Brotherhood evaporate and their supporters turn to others.

Making up half the country’s population of 80 million, Egypt’s illiterate poor cannot be ignored but since a coup overthrew Morsi they no longer have a stake in the political system – and their shadow government has vanished.

They no longer have a leadership structure nor an avenue for local dispute resolution or problem solving. They no longer have adequate service provision from any state or semi-state structure and no longer have any peaceful method of advancement.

But nature abhors a vacuum, and salafist preachers, self-organising militias and organised crime has filled the space. Without access to anything else, people are turning to these groups for everything from social services to medical help, and that is driving their recruiting just as it did for the Muslim Brothers.

This makes the country much more unstable. The old opposition was largely united and could be controlled by pressuring its leadership which had something to lose – that’s why the Brotherhood was so slow to join the revolution. Now a bunch of thugs and extremists whose legitimacy comes from their violent resistance to the government or their criminal acts runs the Upper Nile and the Delta and they are too diverse and with too little a stake in the established order to make any deals worth making.

No where is this more clear than in the Sinai Peninsula where tribal militias are playing host to al-Qaeda affiliated groups while at the same time conducting smuggling operations with impunity. Years of corruption while remembering an old victory in stopping the Israelis from capturing Cairo – after the Israelis had already taken the whole of the Peninsula – have left the army is largely powerless. The generals appear more interested in protecting their massive financial interests than in defending the nation.

So Sisi’s job will be much harder than any of his predecessors’. He won’t be taking over a divided country but a fractured one in which al-Qaeda-linked Salafists compete for influence with mafia-type gangs and tribal militias. In which the police are both the frontline of defence and part of the problem. And one in which the level of violence will steadily increase while the tolerance for any crackdown has diminished both at home and by international partners.

As a military man so reliant on the US, Sisi will no doubt have heard them say: “the enemy gets a vote”. It’s true again in Egypt’s election – not at the ballot box but on the street.

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