All summer, Cairo’s morgues overflowed. Over a thousand people were killed in clashes between Egypt’s top generals and the Islamist supporters of Mohammed Morsi, the Muslim Brotherhood president overthrown in July. Now, as winter descends on Egypt, the military-backed government has shifted its attention to secular activists.

Since November liberal protesters have returned to the streets. Many of them had been in the vanguard of the January 2011 revolution to depose the country’s long-standing dictator Hosni Mubarak. Having been crowded out by Egypt’s two main political actors, the Brotherhood and the military, they wanted to reclaim their own political space. But by early December dozens had been jailed under a new law banning rallies that have not received permission from the interior ministry.

The crackdown on secular protesters has not been as far-reaching or as violent as the attack on Morsi loyalists, but the shift of focus is telling. The military justified crushing the Muslim Brotherhood by arguing that it was necessary in a war against Islamic extremism. “The possibility of a non-Islamist opposition delegitimises the claim of the current interim government that it is facing a wave of terrorism,” Amr Abdel Rahman, a lecturer in law at the American University in Cairo, tells me. For many Egyptians, this marks a return to the Mubarak era.

“Everything is déjà vu,” says the activist and psychiatrist Sally Toma, whose arm is in a sling after police fractured her shoulder at an “illegal” Cairo protest a fortnight ago. Fourteen of her female friends were detained that day, beaten, sexually assaulted and dumped in the desert at midnight – a favoured practice of Mubarak’s security services.

Toma’s street cinema project once worked with the “Rebel” campaign, which called the June protests that toppled Morsi and ushered in the junta. Before the rallies they screened footage of abuses under Morsi’s administration. Now he and much of the Brotherhood’s leadership are on trial, but the judicial proceedings are heavily politicised: Morsi was kept in secret detention for months and five members of his presidential team are still missing.

“Is protesting the only way to go? For three years we have just been chasing each other. You chase your friends in jail, in hospital, then the morgue to find those who died,” Toma says. “But nothing has changed.”

Over 25 prominent secular political activists are facing prison, including the blogger Alaa Abd El Fattah. In late November, 21 women, seven of them teenage schoolgirls, were handed 11-year sentences for protesting in support of the Muslim Brotherhood. Under mounting pressure, the government reduced this to one-year suspended sentences for the 14 young women and a three-month probation for each of the seven minors.

Meanwhile, the government is encouraging the population to focus on the referendum on the new national constitution, due on 14 and 15 January. The document has divided opinion.

“I believe this constitution is more advanced than any other in the history of Egypt,” Mohamed Abul-Ghar, the leader of the Egyptian Social Democratic Party and one of the authors of the document, told me. “The very heavy religious tint in the 2012 [charter] is not there any more.”

Some of the religious articles drafted under Morsi have been removed or toned down, but for Toma the new code replaces “one fascism with another”. The constitution will bolster the power of Egypt’s generals by preserving important military privileges, such as keeping the armed forces’ budget secret and permitting military courts to try civilians. It also stipulates that, for the next two presidential terms, the military must approve the appointment of Egypt’s defence minister. This safeguards the job of Egypt’s de facto leader, General Abdel Fattah el-Sisi.

A successful referendum will be a stamp of approval for el-Sisi. A personality cult has grown around the general. His image has appeared on posters, chocolates, cupcakes, pyjamas and jewellery. One campaign group called Complete Your Favour says it has gathered seven million signatures calling for him to run for president. El-Sisi has yet to give a definitive answer as to whether he’ll stand in the elections, but with few viable alternatives three years on from the overthrow of Mubarak, Egypt may once again have an army officer as its leader.

The activists are not yet disheartened. Much of the protesting has moved into the universities, with secular and Islamist campaigners holding separate rallies daily. “If we don’t use this wave to make the changes we wanted three years ago, then this is going to eat us all,” Toma says. “They say the revolution eats its children.”