The junta at one point seemed comfortable with a political cohabitation with the Muslim Brotherhood, albeit on the generals’ rules. The two sides negotiated arrangements for last year’s referendum and elections, but last spring, their understanding appears to have broken down. And the Shafik candidacy suggests that at least some in the junta would prefer to restore the bureaucratic heart of the old order, precluding any changes that might impede their traditional prerogatives. But announcing a Shafik victory — when the Brothers and their supporters believe they have won the election — could prove to be the final cut for the Islamists, who have seen all their other gains following Mubarak’s fall slashed away or neutered. That could provoke a very dangerous backlash on the street, and a new season of political turmoil that would threaten the generals’ primary goal of stability and potentially unite the Islamist and secular opposition in a common struggle against what would amount to Mubarakism without Mubarak.
A Shafik victory, in fact, may not necessarily be a vital interest to the junta, which could opt for allowing a Morsy presidency in the hope that acknowledging a largely symbolic win by the Brotherhood could defuse a showdown and even give the Islamists a stake in the stability of a new status quo. Even if they challenged military control, the generals would retain a tight rein, and limit the authority of elected institutions. Cohabitation with the regime might even suit the Brotherhood’s leadership, whose appetite for revolutionary confrontation with the security forces has, throughout the 16-month rebellion, been decidedly limited.