Islamist Mohammed Morsi became Egypt’s first freely elected president on Saturday, launching his four-year term with a potentially dangerous quest to wrest back from the military the full authority of his office.

The outcome of the impending battle between Egypt’s first civilian president and its powerful generals will redraw the country’s political landscape after 60 years of de facto military rule.

If Morsi succeeds, the Muslim Brotherhood will likely be emboldened to press ahead with realising the longtime goal of making Egypt an Islamic state. Otherwise the military — which has been reluctant to give up the power it assumed after Hosni Mubarak’s ouster — will continue its stranglehold on the country for years, maybe decades, to come.

For Egypt’s estimated 82 million people, the prospect of a continuing battle between the military and the Brotherhood, the country’s largest political group, will only prolong the political instability that has rocked their nation since Mubarak’s ouster last year. Egyptians have seen the initial euphoria following the revolution turn into a wave of pessimism amid a declining economy, rising crime and a seemingly endless wave of protests, strikes and sit-ins.

Both sides — Morsi and the military — made a show of unity during the inauguration ceremonies that began with the 60-year-old US-trained engineer being sworn in at the Supreme Constitutional Court, then making an address a few hours later at Cairo University as the ruling generals applauded politely.

Morsi repeated his oath of office in the university’s gigantic lecture hall and lavishly praised the military council, which had promised to hand over power to a civilian government by 1 July but pushed through a series of decrees this month that stripped the president of significant powers before doing so.

The decrees gave the military legislative authority after the parliament was dissolved by court order as well as control over the process of drafting a permanent constitution. It also retained its influence on key domestic and foreign policy issues.

The military has already won the first round, forcing Morsi to take his official oath of office before the court because there is no parliament, the traditional venue for inaugurations.

The Supreme Constitutional Court is packed with judges appointed by Mubarak before his ouster and it is the same tribunal that ruled two weeks ago that a third of parliament’s members were elected illegally. Armed with that verdict, the military disbanded the chamber.

The Brotherhood has questioned the legality of the military’s decree and called for the reinstatement of the legislature in which it controlled just under half the seats. Some of the group’s leaders wanted Morsi to be sworn in before members of the dissolved legislature, but the idea was shelved over fears it could unleash a crackdown by the military.

Betraying his anger, Morsi was grim-faced throughout the ceremony, avoiding eye contact with the black-robed judges in the wood-paneled chamber. In a dark blue suit and red tie, he looked straight at the camera rather than the court’s chief judge, Farouq Sultan, as he read the oath.

“We aspire to a better tomorrow, a new Egypt and a second republic,” Morsi said in a brief address to the judges. The courthouse, whose court is a Nile-side structure built to resemble an ancient Egyptian temple, is next door to the military hospital where Mubarak is being held after his transfer from a prison hospital.

The ousted leader is serving a life sentence for failing to prevent the killing of protesters during the uprising that toppled his regime last year.

“Today, the Egyptian people laid the foundation of a new life — absolute freedom, a genuine democracy and stability,” said Morsi after the court ceremony.