It was generally felt in the court that the Emperor should marry and produce heirs as soon as possible. Various potential brides were considered: Princess Elisabeth of Modena, Princess Anna of Prussia and Princess Sidonia of Saxony. Although in public life Franz Joseph was the unquestioned director of affairs, in his private life his formidable mother still wielded crucial influence. Sophie wanted to strengthen the relationship between the Houses of Habsburg and Wittelsbach--descending from the latter house herself--and hoped to match Franz Joseph with her sister Ludovika's eldest daughter, Helene ("Nene"), who was four years the Emperor's junior. However, Franz Joseph fell deeply in love with Nene's younger sister Elisabeth ("Sisi"), a beautiful girl of fifteen, and insisted on marrying her instead. Sophie acquiesced, despite her misgivings about Sisi's appropriateness as an imperial consort, and the young couple were married on 24 April 1854 in St. Augustine's Church, Vienna.  Their marriage would prove to be an unhappy one; though Franz Joseph was passionately in love with his wife, the feeling was not mutual and Sisi never truly acclimatised to life at court, frequently having disagreements with the imperial family. Their first daughter Sophie died as an infant, and their only son Rudolf died by suicide in 1889 in the infamous Mayerling Incident.  In 1885 Franz Joseph met Katharina Schratt, a leading actress of the Vienna stage, and she became his friend and confidante. This relationship lasted the rest of his life, and was--to a certain degree--tolerated by Sisi. Franz Joseph built Villa Schratt in Bad Ischl for her, and also provided her with a small palace in Vienna. Though their relationship lasted for thirty-four years, it remained platonic.  The Empress was an inveterate traveller, horsewoman, and fashion maven who was rarely seen in Vienna. Sisi was obsessed about preserving her beauty, carrying out many bizarre routines and strenuous exercise, and as a result suffered from ill health. She was stabbed to death by an Italian anarchist in 1898 while on a visit to Geneva. A few days after the funeral, Robert of Parma wrote in a letter to his friend Tirso de Olazabal that "It was pitiful to look at the Emperor, he showed a great deal of energy in his immense pain, but at times one could see all the immensity of his grief." Franz Joseph never fully recovered from the loss. According to the future empress Zita of Bourbon-Parma he told his relatives: "You'll never know how important she was to me" or, according to some sources, "You will never know how much I loved this woman."

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She was stabbed to death by an Italian anarchist in 1898 while on a visit to Geneva.