The first time that Mohammed Badie was jailed for his involvement with the Muslim Brotherhood, it was 1965 and his cellmates included Sayyid Qutb, the influential Islamist writer whose arrest and eventual execution by the government propelled modern Egyptian militancy.

Badie, the Brotherhood’s “supreme guide” and top spiritual figure, is now back in the courtroom, and Egyptian officials hope that his latest trial will play out differently — part of a final blow against the Brotherhood rather than just another chapter in the cyclical effort to suppress the group.

The 70-year-old’s arrest “is a clear message — that this is a major confrontation, and it is not just arm-twisting. It is all-out war,” said Emad Shahin, a political science professor at the American University in Cairo and the editor of the “Oxford Handbook of Islam and Politics.”

With a military takeover of the government less than two months old, Egyptian officials on Sunday opened the trial of Badie and other Muslim Brotherhood officials charged with inciting violence and other crimes, the first in what could be a lengthy set of prosecutions stemming from Egypt’s recent convulsion. Badie was jailed as part of a widespread series of arrests — in the thousands, by some estimates — that began last month when the military ousted Brotherhood-backed President Mohamed Morsi and continued Sunday to include affiliates and relatives of the group’s leaders.

Morsi supporters have condemned his ouster as a coup, and it has been followed by clashes that have killed about a thousand people and left the country tense, fearful and under a strict nighttime curfew. Supporters of the military’s crackdown view it as a rescue of the nation from a regime that was becoming increasingly dogmatic and pushing Egypt toward a version of Islamist rule that was stifling to the country’s many Christian and secular citizens.

The trial will prove a prominent extension of that debate as Egypt’s supreme court considers whether the veterinarian-turned-Islamist-scholar and his top deputies should be imprisoned — perhaps even, like Qutb, executed — for events that included a June 30 standoff at the Brotherhood’s headquarters in Cairo in which several protesters were killed. A Brotherhood spokesman had said days earlier that the group had hired private security contractors to guard its headquarters after the Interior Ministry publicly refused to protect it.

As the trial began raucously Sunday, with the judges sitting behind a phalanx of 16 radio and television microphones to offer blanket coverage, defense lawyers said they had no illusion that the proceedings were just about the specific acts of their clients. The trial is part of the broader effort against the Brotherhood, they argued.

“They want to say they are terrorists and demonize the Brotherhood and its leaders so when the coup settles down, the people will be against them,” said Mohammed Attia, an attorney for Badie and two other top Brotherhood figures, Khairat el-Shater and Rashad Bayoumi.

The opening session, held in a dowdy courtroom with a clock stuck at 8:15 a.m., a broken fan and mold-speckled walls, was quickly adjourned until October. With the country unnerved by recent violence, security was such a concern that it was felt that the defendants could not be safely brought from Tora prison, which is on the outskirts of Cairo, to the downtown courtroom.

At the court building, an armored vehicle with a mounted automatic weapon stood at the front while black-clad police officers with riot shields clustered at the entrance and near the front of the courtroom where Badie is to be tried.

Beyond Badie’s trial, the events at the court building on Sunday highlighted the peculiar situation that Egypt finds itself in after the buoyant events of 2011, when a broad popular uprising took root in Cairo’s Tahrir Square and forced longtime president Hosni Mubarak to resign. Near the courtroom where Badie’s trial began, charges against Mubarak also are being heard. As part of that prosecution, Mubarak’s former interior minister, Habib al-Adli, who also is on trial, on Sunday asked that the current military leaders vouch for actions he took during the 2011 protests. Morsi, held at an undisclosed location since his removal from office, also may find himself on trial at some point.

With key members of the last two governments imprisoned, Egypt’s military leaders and the civilian officials they appointed have not indicated who may get the next chance to run the country or how they will be chosen.

The Brotherhood is no stranger to the courtroom. Every Egyptian leader since King Farouk has struggled with the homegrown Islamist organization, at times outlawing it and rounding up its members, at others easing up the pressure in an effort to accommodate.

But the ongoing crackdown has taken on historically broad dimensions — from an intense campaign on state-run television to discredit the organization as an enemy of the people to the arrest of Badie. Local stations are running a steady montage of fiery images from the recent clashes between police and pro-Morsi forces, behind mournful Arabic music with lyrics such as “This is not our country.”

Through all the rounds of arrests over the decades, American University’s Shahin said, the top spiritual figure is targeted only when confrontation peaks.

Badie was not considered a particularly influential Islamist thinker. Like many other top Brotherhood figures, he comes from a scientific and technical background, and his biography on an organization Web site lists no formal religious training.

But because he has ties to the organization that date to one of its formative moments, his trial holds symbolic weight — and may be a clear sign of the lines that the military is drawing for the country’s next phase.

Lara El Gibaly contributed to this report.