A lot has changed in Egyptian politics in the past nine months: There are dozens of new political parties, Islamists are openly campaigning for political power and the most free parliamentary election in decades is underway.

But for some of the people who fought hardest for liberal democracy, the old authoritarian order of Hosni Mubarak lives on. They help explain why Islamists are emerging as the big winners in Egypt’s revolution. Take two cases: Ayman Nour and Alaa Abdel Fattah.

Nour, 47, was a pioneer of democratic politics in the last years of Mubarak’s rule. In 2005 he announced a quixotic campaign for president against the strongman. His reward was to be thrown in jail just as George W. Bush launched his “freedom agenda” for the Middle East. Bush pressured; Nour was freed and went on to run in Egypt’s first contested presidential election. But after he lost the rigged vote, he was quickly convicted on trumped-up charges, and — U.S. protests notwithstanding — sent back to prison for three long years.

Nour finally was released in early 2009 and quickly resumed his political campaigning. A poll this year showed him as one of two potential presidential candidates, along with former Arab League chief Amr Moussa, who have double-digit support. But as part of Nour’s criminal conviction, he was barred from running for office — and he remains blacklisted.

“Mubarak’s shadow is still ruling Egypt,” Nour told me after a long day of canvassing polls in Cairo for his party, called Ghad. “That is especially true of me and the Ghad party. According to the new order, Mubarak’s enemies must still be enemies.”

The same applies to Alaa Abdel Fattah , one of Egypt’s best-known bloggers and political activists, who was jailed in 2006 by Mubarak — and now is once again imprisoned and facing trial in a special security court. On Monday, even as Egyptians began voting, a prosecutor charged Abdel Fattah with a string of serious crimes, including incitement to terrorism.

His real offense, as in 2006, was free speech. In October, the indefatigable activist published a searing newspaper column that described the scene in a hospital morgue after more than two dozen people had been killed in Cairo by troops who attacked a march of Christian protesters. The military responded to the intense resulting criticism by arresting Abdel Fattah and claiming — ludicrously — that he had stolen a military weapon and attacked troops.

“I never expected to repeat the experience of five years ago,” Abdel Fattah wrote in a letter from jail, published Nov. 1. “After a revolution that deposed the tyrant, I go back to his jails?”

Nour and Abdel Fattah have something in common besides their history of fighting the Mubarak regime. Both are committed secularists and supporters of liberal democracy in Egypt. That makes them more, not less, of a target for the ruling military council. Like Mubarak, the generals who replaced him are willing to cut deals with the Muslim Brotherhood and other Islamic groups — while seeking to marginalize secular alternatives they do not control.

The goal is to present Egyptians — and Western allies such as the United States — with a stark choice: rule by Muslim fundamentalists or continued reliance on the military. The initial results of the parliamentary elections will likely reinforce that strategy. Islamist parties are winning more than 60 percent of the vote so far, which could give them a commanding position in the new parliament.

Like many other secular democrats I spoke to this week, Nour suspects the generals will make a deal to share power with the Muslim Brotherhood after the elections while continuing to persecute the liberals.

The generals “are playing with the Brotherhood and sending the message to the United States that it is us or them,” Nour said. “We as liberals pay the price. It is exactly the same strategy that Mubarak pursued. Only this time no one understands we have a problem, because supposedly all the problems have been fixed by the revolution.”

Leaders of the Muslim Brotherhood respond by saying that the elections are showing they command the political majority in Egypt — so it is only logical that they be the leading interlocutors with the military council. Yet their majority is the product, in part, of 60 years of authoritarianism in which the only groups allowed to organize were Islamic movements.

The liberals argue that secular forces remain the real majority in Egypt and could defeat the Islamists in a free political competition. But first, they must be given a level playing field. It’s hard to win an election if you are banned from the ballot — or in prison.