Hosni Mubarak and his sons may have been arrested, but troubling signs are emerging from Egypt. While the faces have changed, the state apparatus and its institutionalized hierarchy of domination still appears to be intact. Yesterday, a military court in Cairo sentenced Maikel Nabil to three years in prison for insulting the military in a series of critical blog posts.

Earlier this month, the Egyptian army was engaged in a violent crackdown on the largest post-Mubarak protest in Tahrir square, killing two. Thousands of people had converged upon the square to ‘safeguard’ the Revolution and protest against the army’s handling of the transition to genuine democracy. The crackdown and the arrest are raising the question if the Egyptian Revolution might have been stalled in its tracks, or even stillborn to begin with.

Certainly enormous challenges lie ahead. To the astute observer and the intelligent Egyptian activists, it was always clear that overthrowing Mubarak was the easy part. Replacing any institutionalized system that is atrophied by corruption, entrenched by multi-billion dollar financial interests, and defended by a well-organized and well-funded military, is a lot harder than merely replacing the face at the top of the political pyramid scheme.

Clearly, Mubarak was forced to leave not because the people told him to, but because the military told him it would no longer support him against the will of the people. Any political ruler, whether democratic or dictatorial, relies (to varying degrees) on the two great pillars of power: military force and popular legitimacy. Without the latter, the former easily slips from your hands. Without the former, the latter can easily be overturned by a more powerful opponent.

While it would be premature to say that the Egyptian Revolution has stalled, it was even more premature to assume it to have been completed with the fall of Mubarak. To bring about genuine democracy, Mubarak — as the symbol of oppression — had to go, but he was dispensable. In this respect, chanting for the fall of the regime was only the first step — the system of power still needs to be dismantled, and a new one will have arise on top of it.

It was always naive to assume that the Arab Spring was just going to be about democratic love birds and the innocent tweets of revolution. Revolution is a painful process of radical change that at many points will be set back by counterrevolutionary movements and political infighting. The French Revolution of 1789 was followed by multiple relapses into dictatorship, not least that of Napoleon Bonaparte — who ruled twice! — and his nephew, Napoleon III.

Egypt’s pro-democracy activists are facing their greatest challenge so far: how to upend the essentially oppressive institution of the military, which is so revered around the country and which continues to be such an important bulwark against an Islamist takeover. The arrest and sentence of Maikel Nabel is an unmistakable signal of who’s still in control. But even the military leadership knows that without popular legitimacy, it is nothing. With this in mind, the Egyptian people will simply need to keep pushing.

As Stephen Gill has put it, “history is always in the making, in a complex and dialectical interplay between agency, structure, consciousness and action.” The consciousness of the masses has already been lifted, the agency of the people affirmed — now is the time to take more action and ensure that the fundamental power structure changes along with everything else. This is still history in the making.