CAIRO — Egypt’s authoritarian government has harassed and repressed the Muslim Brotherhood for most of its existence. But for the last three decades the authorities stopped short of touching the group’s revered leader, the supreme guide, who oversaw the country’s most effective social, political and religious organization despite its outlawed status.

On Tuesday, the new government installed by Gen. Abdul-Fattah el-Sisi provided the latest signal that it was breaking the old rules. Security forces armed with automatic rifles hunted down even the supreme guide, Mohamed Badie, 70, in a nondescript apartment where he had taken refuge, and then provided footage of the arrest to a friendly satellite network.

It was the capstone of a sweeping campaign of arrests and shootings that has damaged the Brotherhood’s core organization more than any crackdown in eight decades, sending the group into a confused retreat deeper underground than ever before.

“We came close to annihilation once under Nasser, but this is worse,” said Gehad el-Haddad, a Brotherhood official now on the run, referring to former President Gamal Abdel Nasser’s attempt to smash the group after he came to power in 1954. Communicating over the Internet to avoid surveillance, Mr. Haddad said Brotherhood members now talk of “the good old days” under President Hosni Mubarak.