In the weeks before his death, Boudiaf made powerful secular enemies inside Algeria - at least one of them reportedly linked to the former president, Chadli Bendjedid - and even his widow now says she does not believe the Islamic Salvation Front (FIS), initially blamed for his murder, committed the crime.
Boudiaf was killed by one of his own bodyguards, Second Lieutenant Lembarek Boumaref, while addressing a public meeting in the eastern Algerian city of Annaba on 29 June. State television cameras were taping Boudiaf's address at the moment of his death and General Larbi Belkheir, the interior minister sacked earlier this week, later announced that Boumaref acted alone. Boudiaf was killed by three bullets, two of which hit him in the head and a third in the back.
Boudiaf returned from exile in Morocco to lead Algeria after the resignation of Mr Chadli and the suspension of the second round of parliamentary elections last January - elections which the FIS, demanding an Islamic republic in Algeria, were certain to win. The FIS were thus the first to be suspected of the murder, especially when the Islamic party's supporters abroad expressed satisfaction at Boudiaf's death.
However, there are now rumours in Algiers that Boudiaf - against the wishes of the more intransigent members of the government and military - was trying to open a dialogue with moderate FIS officials. More importantly, it is known that he had embarked on an anti-corruption campaign that had already netted a retired Algerian army major-general and a prominent businessman and associate of Mr Chadli in the southern city of Tamanrasset. And only days before Boudiaf was assassinated, a senior officer responsible for one of the investigations was himself mysteriously murdered.
Some of the television tape of Boudiaf's killing, it is now clear, was suppressed by the authorities. Eyewitnesses claim that four separate television cameras taped the scene at the moment of the president's assassination. A source close to the state Algerian Television Service has confirmed to the Independent that the tape shown on television around the world, in which Boudiaf could be seen uttering his last words and then lying dead on the ground with blood on his chest, was censored.
'The cameras filmed the actual moment of the killing and they censored the scene when the bullets hit Boudiaf,' the source said. 'The tape showed his brain exploding when the bullets hit him in the head - you cannot show something so terrible on television. There is another tape which shows the arrest of Boumaref. In this, Boumaref says on camera: 'I killed Boudiaf knowing of his heroic past and that he was a good man. But he didn't do enough against the mafia. And he opposed the choice of the people. I belong to no political party but I belong to the Islamic movement.'
'Boumaref was so self-confident, so sure of himself - he spoke so well and was so charismatic - that the authorities feared he would become a hero if the tape was shown on television.'
If this account is correct, then Boudiaf's murder may indeed have involved the Islamic movement. But the events surrounding Boumaref's arrest are extremely puzzling - especially if the authorities really believed him to be a fundamentalist murderer. One account says that he was able to escape from the Annaba conference hall but later surrendered peacefully to the police. Curiously, the army - which tried the civilian leaders of the FIS in a well-publicised court hearing in Blida last week - refused to take responsibility for Boumaref, claiming instead that he must be tried by a civilian court.
Boumaref is thus now incarcerated in the civilian prison at Annaba, and local journalists have been able to discover little about his family or background. He is 26 years old and, so it is rumoured, used to be an official bodyguard for Mr Chadli. The Independent has been told that Boumaref was trained for his job in the presidential security unit by the Italian carabinieri.
It is Boudiaf's actions in the days and months before his assassination, however, that may provide the most valuable clues to his murder. He was brought back to Algeria by the military-backed Higher State Council - formed after the suspension of elections - in order to crush the FIS and restore order. He promised a war against violence but also against corruption, and appears to have kept his word.
Perhaps to the surprise of the former ruling party, the FLN, and army hands who originally supported him, Boudiaf in May ordered the arrest of the retired major-general, Mustapha Beloucif, who was charged before a military tribunal at Blida with misuse of state funds. Maj-Gen Beloucif was dismissed from his job as secretary-general at the Algerian Defence Ministry in 1987; in 1989 a five-man military inquiry - including the man who is currently the Defence Minister, General Khaled Nezzar - is reported to have investigated the misuse of more than dollars 6.6m ( pounds 3.5m).
Boudiaf also ordered the arrest of a prominent Tamanrasset businessman on corruption charges. The man, who is said to have twice hosted Mr Chadli in Tamanrasset, was allegedly involved in the illegal sale of subsidised food to Niger and Mali and in the smuggling of drugs and weapons. One of the officers dispatched to Tamanrasset to carry out the investigation was a lieutenant-colonel in the security forces - and only days before Boudiaf's murder, the colonel was assassinated in Algiers.
An official government inquiry is to present a full and public report on Boudiaf's killing today. The investigating committee includes two friends of Boudiaf, four lawyers and the head of the Algerian League of Human Rights. But already one columnist has dubbed the assassination 'Algeria-gate' and hinted that Boudiaf's death may be covered up like the murders of the FLN dissidents Mohamed Khider, shot in a Madrid street in 1967, and Krim Belkacem, strangled in a Frankfurt hotel in 1970.
In the daily El Watan, the journalist Laid Zaghlami recalled that the Algerian government inquiry into the death of Mohamed Benyahia - the Algerian envoy shot down along with his delegation over the Iran-Iraq frontier during an attempt to end the Gulf war - was kept secret 'to protect the nation's supreme interests'.
It is now popular in Algeria to attribute Boudiaf's assassination to the mafia - an opaque term generally used to indicate the social and political class that enriched itself at the expense of the country during Mr Chadli's 12- year rule. The authorities are leading what amounts to a campaign to discredit Mr Chadli, whose whereabouts are not publicly known.
The claim of the former prime minister, Abdul-Hamid Brahimi, that bribes of dollars 26bn - the equivalent of the country's foreign debt - were paid to government officials over a decade has entered popular folklore. Supporters of the government insist there is an alliance between the mafia and the Islamic fundamentalist movements. But, of course, they can produce no proof.