Pope Shenouda III, the head of the Egyptian Coptic Orthodox church for 40 years, has died in Cairo after a long illness at the age of 89.

His death comes at a particularly tense moment for Egypt’s estimated 8 million Christians who feel they face an uncertain future as Islamists of various stripes from moderates to ultraconservatives have come to dominate politics following last year’s overthrow of Hosni Mubarak, the former president.

A charismatic man who enjoyed the respect of large swaths of the Egyptian population, Pope Shenouda steered the Coptic Church through four difficult decades marked by increasingly frequent eruptions of deadly sectarian violence targeting Christians.

In 1981, Anwar Sadat sent him into internal exile at a desert monastery because he criticised the former president for failing to rein in Muslim extremists carrying out attacks against Christians.

The Pope had already angered Sadat by banning Copts from travelling to Jerusalem to visit Christian holy places after Egypt signed its peace deal with Israel in 1979. Aware that the peace had many opponents at home and in the region, he feared that allowing his community to visit Israel would deepen divisions with Muslims and open Copts to accusations of lacking patriotism.

His insistence that his flock would only go to Jerusalem after Palestinian rights had been restored earned him lasting respect in Egypt and across the Arab world.

The Pope’s internal exile lasted until 1985 when Sadat’s successor, Hosni Mubarak, lifted the restrictions on him.

Thereafter, the Christian leader eschewed public confrontation with the country’s rulers, preferring to resort to back channels to negotiate solutions to the problems of Copts who were facing rising sectarianism. He also came to regard the Mubarak regime and the ruling National Democratic party as bulwarks against Muslim extremism.

In practice, this meant the church pledged its political support and that of its millions of loyal followers to Mr Mubarak and the NDP to ensure a measure of protection for Christians. In recent years, however, the regime’s guarantees looked increasingly frayed as Christians faced huge difficulties obtaining government permits to build churches and as the frequency of attacks increased.

In addition, the close relationship between the Coptic church and the Mubarak regime, particularly its all-powerful security services, sometimes turned into a liability provoking Muslim anger against the church. On two occasions in recent years, public opinion was outraged when police handed over to church officials the wives of priests who had wanted to convert to Islam in order to divorce their husbands.

Divorce is severely restricted by the Coptic Church, which became even more socially conservative under the leadership of Pope Shenouda. He led changes to the rules abolishing all possible grounds for the granting of divorce except for adultery.

Although deeply revered by his community, since the revolution Pope Shenouda started to face the beginnings of dissent from young Christian activists frustrated at what they saw as the failure of the Church’s soft approach to ensure the community’s rights. Activists have organised demonstrations and sit-ins, in defiance of the Pope’s orders, to protest against attacks targeting churches.

As the news spread of the Pope’s death on Sunday, thousands of Egyptian Christians congregated at the main Cairo cathedral to mourn the only head of church most of them have ever known. A new leader will be chosen in the coming weeks according to ancient procedures, but already it is known that there are power struggles behind the scenes focusing on the succession.

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