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After the Execution of Louis XVI, the French Republic was in a war against many European countries. As the threat of a counter-revolutionary's plot rose, Maximilien de Robespierre, head of the Jacobins and of Committee of Public Safety, orchestrated of the Reign of Terror to eliminate the enemies of the Revolution. The other goal of the Terror was to accomplish the Great Work of the Sage and Grand Master of the Parisian Rite of the Templar Order François-Thomas Germain who wanted to reshape humankind by fearing liberty.
The Templar Élise de la Serre and her lover the former French Assassin Arno Dorian allied to stop Germain as he assassinated Élise's father François de la Serre. To reach Germain, the two decided to discredit Robespierre and interrogate him. During the festival of the Supreme Being, Élise poisoned Robespierre with ergot to make him look like a mad man. Arno recovered a list of deputies from the National Convention wrote by Robespierre. Arno sent the document to deputies who thought it was a list of individuals that Robespierre wanted to execute.
On 10 June 1794, Robespierre increased the Terror, calling for a purge of all the members of government who perpetrated massacres around France. The deputy Jean-Lambert Tallien led a group of deputies and the Convention voted for the arrestation of Robespierre and his acolytes on 27 July. The National Convention arrested Robespierre under the charge of treachery until he was rescued by his troops of the Paris Commune and taken to the Hôtel de Ville.
Robespierre was declared an outlaw and members of the National Guard, commanded by Paul Barras, were sent after him. As Arno and Élise wanted to discover Germain's location, they infiltrated the Hôtel de Ville to interrogate Robespierre. As he refused to speak, Élise shot him in the jaw. Robespierre then wrote the location of his master, the Temple. As the lovers left the place, Barras' forces overpowered the Jacobins and managed to recapture Robespierre, alongside his closest allies, Louis Antoine de Saint-Just, Georges Couthon, François Hanriot, and Augustin Robespierre. The next day, Robespierre and his allies were executed, putting an end to the Reign of Terror.
The same day, Arno and Élise confronted Germain in the Temple. The Grand Master was in possession of a Sword of Eden, a Piece of Eden. During the fight, the sword projected an energy blast that killed Élise and wounded Germain. Arno, who witnessed the death of his lover, killed Germain remorselessly. In his final confession, Germain explained all what he did to Arno and that, even if he died, someone else would take control of the new society he created. After that Arno left the Temple carrying Élise's body and kept the depowered Sword of Eden.
On the night of July 29, Théroigne de Méricourt led an attack of the convent of Jacobins where the last remnants of Germain's faction took refuge. The Assassins helped Théroigne and killed the Jacobin leaders, ending their control on France.