One of the major innovations the Republic hoped to achieve was enshrined in its constitution: freedom of religion, with Pope Pius IX and his successors guaranteed the right to govern the Catholic Church.

On the night of 24 November, Pope Pius IX left Rome disguised as an ordinary priest, and went out of the state to Gaeta, a fortress in the Kingdom of the Two Sicilies.

This delegation was composed of the mayor himself, Prince Tommaso Corsini, three priests – Rezzi, Mertel and Arrighi – Marchese Paolucci de Calboli, doctor Fusconi and lawyer Rossi.

[4] The Costituenti decided to schedule direct and universal elections (electors were all the citizens of the State, male and over 21 years old) on the following 21 January 1849.

Since the pope had forbidden Catholics to vote at those elections (he considered the convocation of the election "a monstrous act of felony made without a mask by the sponsors of the anarchic demagogy", an "abnormal and sacrilegious attempt... deserving the punishments written both in the divine and the human laws"), the resulting constitutional assembly (informally known as "The Assembly of the Damned")[5] had a republican inclination.

It included twenty-seven owners, a banker, fifty-three jurists and lawyers, six graduates, twelve professors, two writers, twenty-one doctors, one pharmacist, six engineers, five employees, two merchants, nineteen military officers, one prior and one monsignore.

When news reached the city of the decisive defeat of Piedmontese forces at the Battle of Novara (22 March), the Assembly proclaimed the Triumvirate, of Carlo Armellini (Roman), Giuseppe Mazzini (Roman) and Aurelio Saffi (from Teramo, Papal States), and a government, led by Muzzarelli and composed also by Aurelio Saffi (from Forlì, Papal States).

Saliceti and Montecchi left the Triumvirate; their places were filled on 29 March by Saffi and Giuseppe Mazzini, the Genoese founder of the journal La Giovine Italia, who had been the guiding spirit of the Republic from the start.

However, the government's policies (lower taxes, increased spending) were fiscally expansionary and involved a decrease in the value of the currency.

He himself had participated in an insurrection in the Papal States against the Pope in 1831, but at this point, he was under intense pressure from ultramontane French Catholics, who had voted overwhelmingly for him.

Thus, though he hesitated to betray Italian liberals, Louis Napoleon ultimately decided to send French troops to restore the Pope.

On 25 April, 1849, some eight to ten thousand French troops under General Charles Oudinot landed at Civitavecchia on the coast northwest of Rome, while Spain sent 4,000 men under Fernando Fernández de Córdova to Gaeta, where the Pope remained in his refuge.

The French sent a staff officer the next day to meet with Giuseppe Mazzini with a stiff assertion that the pope would be restored to power.

Neapolitan troops sympathetic to the papacy entered Roman Republic territory, and de Lesseps suggested that Oudinot's forces in their current position might protect the city from the converging approach of an Austrian army with the Neapolitan force: the Roman Triumvirate agreed.

According to Raffaele De Cesare: The Roman question was the stone tied to Napoleon's feet – that dragged him into the abyss.

He never forgot, even in August 1870, a month before Sedan, that he was a sovereign of a Catholic country, that he had been made emperor, and was supported by the votes of the conservatives and the influence of the clergy; and that it was his supreme duty not to abandon the pontiff.