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Ali Hamdan composed himself and began leafing through a dusty, frayed ledger book. "I'm sorry, Dr. Ibrahim," he finally said. "We are simply full. We've got a full house, after the arrest of the followers of Sheikha Manal." (The Sheikha, a Cairo housewife, had recently been accused of heresy.) The old man continued going up and down his list: Gama'a al-Islamiya, al-Jihad, the Muslim Brotherhood. It was a veritable who's who of Egypt's Islamist groups.

After a good deal of telephoning - it was the weekend, and no one was picking up - Ali Hamdan finally found someone, who found someone else, who agreed that, since according to the prosecutor's order, Saad Eddin was to be kept in solitary confinement, he should be dispatched to the prison's hospital ward. It was empty, and on that Saturday night in Cairo, everything else was full.

HAD SEEN Saad Eddin Ibrahim in many personas over the years: as my professor of sociology at the American University of Cairo in the late 1970's; as a friend; as a consultant to the United Nations and the World Bank; as an irascible interlocutor, who favored silk ascots and ties, pounding his fist on a lectern at the Council on Foreign Relations in New York or, with equal skill, puncturing the arguments of a trembling government official on television screens across the Arab world. And yet, it was not until a sunny morning in the late days of April this year, with his trial under way, that I had ever imagined seeing him sitting inside a cage.

In fact, it was the same cage - or perhaps a similar one - in the same High Security Court where the Islamist assassins of the previous Egyptian president, Anwar Sadat, had been tried and sent to their executioners some 20 years before. The symbolism was not lost on any of us sitting in the court. It was that assassination that had led a young Hosni Mubarak, freshly installed as president and brandishing his emergency laws, to establish not only these High Security Courts - against which there is no appeal - but also Emergency Courts and Special Military Courts. All of these have been decried over the years by human rights groups as contrary to all precepts of international law.

In the 1990's, the courts played a crucial role in Mubarak's successful campaign to crush a rebellion by Islamic militants. Thousands of Islamists, alleged Islamists and would-be Islamists were summarily arrested under emergency law and paraded in and out of these courts and their cages, and they continue to be. Even today, between 15,000 and 16,000 Islamists -- not all of them militants -- remain in prison. Many have never been charged or tried. Under Mubarak's emergency laws, his regime is not even obligated to release their names.

As long as the courts were employed -- ostensibly at least -- against Islamic militants, the West was more than happy to look the other way. But with the arrest and trial of Saad Eddin, Egypt's increasingly powerful security services seemed to have widened their brief, dangerously. For this was the first time, at least that anyone could recall, that a liberal was being tried by one of Mubarak's extraordinary courts. And he was not only a liberal but also the West's favorite Arab intellectual and his country's most prominent human rights and democracy advocate, arguing passionately for an opening to democracy, civil rights and the rights of Egypt's Christian Copts, a minority suffering frequent discrimination. And he had even served occasionally as an adviser to the Egyptian president himself.

HE ABSURDITY OF THE cage in which Saad Eddin Ibrahim now sat -- a giant metal one along a wall of the room, with planks of wood haphazardly criss-crossing its top, in which the defendants were locked while the court was in session -- was, in a sense, a metaphor for his trial. There he was forced to defend his innocence against a sweeping indictment that neither he nor his lawyers were fully able to comprehend. (It appeared to be contrary to at least two Egyptian laws and legal precedent.)

For months on end, he listened in pained silence to accusers he did not know, and who had never read his books, but who charged nevertheless that he had "tarnished" Egypt's image abroad. He looked on in disbelief as he was accosted with charges of financial impropriety that were based exclusively on the testimony of one of his associates, who later recanted everything he said and ultimately sat with Saad Eddin inside the metal cage, as a co-defendant.

When the state finally presented its case, it charged Saad Eddin not only with defaming Egypt but also with accepting money from abroad without government approval, embezzling donated funds and conspiring to bribe officials from government-controlled television and radio. (Ultimately, everyone would be acquitted of the bribery charge, after those named as the would-be recipients testified that not only did they not know Saad Eddin but also that most of them didn't even work for state radio or television.)

The defamation count stemmed from the professor's writings and lectures on clashes between Egypt's majority Muslims and the Copts and on his findings of voting irregularities in 88 constituencies during parliamentary elections in 1995. (It is worth noting that eight days after Saad Eddin's arrest, the Supreme Constitutional Court declared the entire Parliament invalid because of electoral irregularities, and that other writers had published reports on discrimination against the Copts without being brought before Mubarak's courts.)

The charge of accepting money from abroad without the government's permission was rooted in a $250,000 grant from the European Commission to, in part, produce a documentary film on voter registration and education and on the importance of participating in last autumn's poll. That charge was in turn grounded in a 1992 military decree that had been hastily promulgated to prevent Islamist organizations from providing assistance to victims of a devastating Cairo earthquake.

The issue of the constitutionality of that law is now pending before the courts. But it hardly seemed germane to Saad Eddin's trial, since the law applied only to nongovernmental organizations and charitable groups, not to a research center, like Ibn Khaldun, that had long been registered (and paid taxes) as a civil company.