The prosecutions are the next phase in a wide-ranging crackdown on the Brotherhood following the military's July ouster of President Mohammed Morsi, who goes on trial next month.
Morsi's trial, the most high-profile case, is setting a pattern for the others, aiming to show that the Brotherhood leadership directed a campaign of violence. Morsi is charged with inciting murder in connection to a protest during his year in office in which his supporters attacked protesters outside his palace.
Leaders may also be charged with fomenting violence in post-coup protests by Morsi's Islamist supporters demanding his reinstatement. Security forces have cracked down heavily on the protests, claiming some participants were armed, and have killed hundreds of Morsi backers. With each new round of protests and violence, prosecutors consider new charges that include incitement and arming supporters, Brotherhood lawyers say.
So far, at least nine and possibly more than a dozen cases are being put together, according to a prosecution official and Brotherhood lawyers.
Brotherhood lawyer Mohammed Gharib denounced the cases as simply "a fig leaf by authorities to cover over their scandal"—to justify the coup and the crackdown, pointing out that no police have been investigated for killing protesters. "They are going after their main political opponent," he told The Associated Press last week.
On Friday, the Brotherhood legal team said Gharib left the country for security reasons and has been replaced by another lawyer. Dozens of Brotherhood lawyers have already been detained. Gharib, himself tried under previous administrations, represented the Brotherhood's jailed top leader Mohammed Badie and other senior members.
Some 2,000 high- and middle-ranking Brotherhood figures have been detained, and Gharib estimated another 6,000 rank-and-file members and supporters are also in custody, being questioned for material to use against the leadership. Among the biggest figures in custody are Morsi, Badie and his deputy Khairat el-Shater, and almost half the group's main leadership council and many of its former parliament members. Rights lawyers say they are struggling to keep track, given the high numbers jailed and prosecutors who are keeping a tight lid on information.
Even rights lawyers who see a strong basis for prosecuting Brotherhood figures over violence and abuses of power expressed concern over the scope of the projected trials. Rights advocates have called for a thorough program of transitional justice to address abuses from the time of autocrat Hosni Mubarak and through the past 2 1/2 years of Egypt's turmoil since his ouster—which would also mean trying police and military officials for killing protesters and other rights violations.
Instead, they fear unfair trials with shoddy evidence will be used for the political aim of undermining the Brotherhood.
"They want revenge," Amr Imam, a rights lawyer with the Hesham Mubarak Legal Center, said of the current authorities. "The rights of not only the Brotherhood, but many other Egyptians, will be lost because of arbitrary procedures."
The Brotherhood, which despite being illegal grew in recent decades to become Egypt's best organized political group, leaped to power in elections after Mubarak's 2011 ouster. The presidency of Morsi, a Brotherhood member who became Egypt's first freely elected leader, prompted a massive backlash from many in the public who saw the group as trying to monopolize power and impose its vision on the country.
The military removed Morsi on July 3 after protests by millions against him. The group says the military has crushed the country's fledgling democracy and will bring back Mubarak-style rule.
During its 85-year history, the Muslim Brotherhood has seen frequent waves of arrests. But this time is different.
Under Mubarak, Brotherhood leaders at times were jailed under emergency laws on accusations of belonging to a banned group, but were only occasionally brought to trial. Instead, their detentions and releases were part of a political game, used by the regime to wrest concessions from the group, particularly ahead of elections.
"We used to play chess with the previous regime," said Gharib. "Now it is straight out crushing."
Gharib also noted another difference—in the past 30 years under Mubarak, there was no attempt to associate the group with violence.
The major exception was a high-profile military trial of Brotherhood figures under Mubarak, in 2008, when 25 members, including senior leaders and financiers, were sentenced to up to 10 years for money laundering and terrorism. The case was initiated after masked Brotherhood students held a militia-style demonstration in Cairo, raising an investigation into whether the Brotherhood had resurrected its military wing.
A prosecution official said nine or 10 cases are so far being prepared on incitement and other charges. Investigators are citing recordings of conversations among leaders plotting violence, testimonies by victims of violence and weapons seized at two pro-Morsi protest camps, according to the official, who spoke to AP on condition of anonymity because he is not authorized to talk to the press.
Morsi's trial begins on Nov. 4, with 14 other Brotherhood figures as co-defendants. Their case is rooted in an attack by Brotherhood supporters on an anti-Morsi protest camp outside his palace in December, during his presidency, which sparked clashes that left 10 dead. Morsi is accused of inciting his followers to attack the protesters, a charge that could carry the death penalty.
Morsi has been held in a secret military detention with no access to his lawyers and has refused to cooperate with investigators. In leaked reports of his interrogations, Morsi insisted he is the legitimate leader of the country. His family called the trial and accusations "laughable."
The trial of Brotherhood leader Badie began in August. He, his predecessor Mahdi Akef and senior deputies are charged with incitement in connection to an incident days before Morsi's ouster, when Brotherhood members opened fire on anti-Morsi protesters outside the Brotherhood's Cairo headquarters, allegedly intent on storming it. At least eight people were killed.
In interrogation transcripts leaked to the press, the 85-year-old Akef is questioned about testimony by a journalist at the clashes who claimed to have overheard a Brotherhood member talking to Akef on the phone, asking for more weapons.
"These are lies," Akef replied, saying the investigators should be tried for putting together "baseless" accusations, according to the Al-Fagr newspaper.
Badie is also being investigated in a separate case. A few days after Morsi's ouster, his supporters rallied outside a Republican Guard facility where they believed he was detained. Authorities say they tried to break in after Badie and a prominent pro-Brotherhood preacher Safwat Hegazy urged protesters in public speeches to free the ousted president. In the ensuing violence, security forces killed 51 protesters, and a military officer and two policemen were allegedly killed by armed protesters. Hegazy is also jailed now under investigation in the case—and on trial in a separate one.
Gharib said that top Brotherhood figures were told by prosecutors during questioning that they were accused of trying to topple the regime, which he found ironic because the group considers Morsi to be the legitimate president.
Another Brotherhood lawyer, Osamal el-Helw, said with each new instance of violence around ongoing protests, Brotherhood leaders are added to new investigations, presumably on incitement charges. He said Badie, who has been interrogated in over a dozen cases, will likely face more trials.
The question of how intensely authorities will carry out prosecution and trials is tied up in political considerations, rights lawyers say.
Seif, who represented Brotherhood members in past cases, said he believes the aim is to win criminal sentences that would prevent Brotherhood figures from running in any parliament or presidential elections next year.
Imam believes the flurry of investigations is a pressure tactic to force the Brotherhood to rein in more extremist allies, who have carried out attacks on churches, state facilities and troops in Sinai.
"It is not the Brotherhood that are carrying the weapons," he said. "They are part of an alliance of radical groups who are, and the Brotherhood speaks for them now."