It was claimed by, among others, Empress Zita, widow of the last Emperor, Karl (r: 1916-1918), that the Crown Prince was killed either at the behest of Austrian security officials for his suspected pro-Hungarian sympathies or by French agents because he refused to participate in the deposition of his pro-German father, Emperor Franz Josef. No evidence has been discovered to prove either of these theories, though an examination of the remains of Marie Vetsera (which had been stolen in the early 1990s and on rediscovery were checked to ensure they were the correct remains) contradicted the official reports that she had been shot; her skull showed no evidence of bullet wounds or shrapnel. Instead the evidence was that she had been beaten to death.
A resulting re-examination of files about the death of the Crown Prince revealed major discrepancies between the claimed manner of the deaths and the factual evidence, including that Rudolf had engaged in a violent struggle prior to his death, that the gun that caused his death was not his, and that six shots were fired from the gun. How someone who had reportedly died instantly from the first shot managed to fire the remaining five bullets remains a mystery.
While the official statement of how the deaths occurred and its central theory of a double suicide is now discredited, it remains unclear whether Rudolf in fact battered his mistress to death before killing himself. And if he did, how he managed to shoot six bullets when the first would have instantly caused his death. Also open to suggestion is that both were killed by a third party. No other source material is available to establish just what did happen.
Empress Zita, who was the last surviving confidante of Emperor Franz Josef and may have been able to shed some light on the private opinions of the members of the Hapsburg family and their advisors, died in 1989.