The worst day of violence was on Jan. 28, with hours of deadly clashes with police. Video footages from that day showed police trucks running over demonstrators and policemen using what look like firearms against the unarmed protesters. By the end of the fighting, police were broken and withdrew from the streets for most of the rest of the uprising — and they have only partially returned.
The days that followed saw violence whose source was murkier — though protesters blame security forces or Mubarak supporters.
Snipers shot protesters from rooftops or rained rocks and firebombs on them. Men armed with swords and whips and on the back of camels and horses waded into the crowds at Cairo's central Tahrir Square, the epicenter of the uprising. There were also attacks on police stations and jails, freeing thousands of convicts who fueled a dramatic surge in violent crime across Egypt.
But revealing the truth could also bring troubles for Morsi, of the Muslim Brotherhood. It could increase pressure on him to go after suspects in the security agencies, whose goodwill he now needs to cement his government's shaky hold.
Some in the Interior Ministry, which runs the police, have already seemed the resist the rule of the Brotherhood, which is the backbone of Morsi's presidency. During Mubarak's rule, the Brotherhood was the regime's top nemesis and security agencies frequently targeted it in crackdowns.
Recently, Brotherhood officials have criticized police for failing to protect offices of the group that were attacked by protesters during unrest in November and December over the new constitution. The criticism may have been one reason behind the replacement of the interior minister in a Cabinet reshuffle this month.
But moving to prosecute police officers could bring a backlash from security officials Morsi needs right now.
Morsi's tenure has been defined by an enduring lack of security, with police still not fully acting against crime. At the same time, Morsi, who won election in June by a narrow 51 percent of the vote, faces sharp pushback from a liberal and secular opposition that accuses he and the Islamists are recreating the Mubarak dictatorship with a religious slant.
Morsi's troubles are likely to grow when he introduces unpopular economic measures to prop up the country's faltering finances, including reducing huge state subsidies on fuel and hiking taxes and prices to secure a $4.8 billion IMF loan.
Legal expert Nasser Amin said the new trial would proceed in a much less charged atmosphere than the first one, when Mubarak loyalists and relatives of the killed protesters often clashed outside the courthouse.
Attention may be more distracted by campaigning for important parliamentary elections expected to be held in April.
"These elections constitute the only hope to achieve a balance between the country's political forces," said Amin, alluding to the domination by the Islamists of the first parliamentary elections held in late 2011 and early 2012.
"It will be a very intense fight."