Within the guarded walls of the Palestinian presidential compound, known as the Muqata, the body of Yasser Arafat lies inside a gleaming limestone and glass mausoleum. It is here that political figures, dignitaries, devotees and tourists come to pay their respects to a man who was revered and reviled across the world as the face of the Palestinian struggle for decades.

The mausoleum is closed to visitors for renovations to the Muqata. So the next group to cross the smooth pale flagstones between the compound's southern gate and Arafat's tomb is likely to comprise three French judges, expected to arrive in Ramallah in the next few weeks. Their mission is to investigate allegations that the former Palestinian president did not die of natural causes but was murdered (video), poisoned by agents acting for Israel.

There has been no shortage of rumours and theories about the cause of Arafat's death in November 2004, following a sudden deterioration in his health after more than two years of virtual incarceration inside the Ramallah compound. Claims that the 75-year-old leader had Aids or cirrhosis were swiftly discounted, but suggestions that he was poisoned have proved more durable. Now scientists are attempting to prove or quash such theories.

The exhumation of Arafat's body will be a delicate and emotive undertaking, given the deep affection and respect in which he continues to be held by Palestinians almost eight years after his death. The corpse will be removed from the tomb and transferred to a hospital in Ramallah for samples to be taken and tested for the presence of toxins.

According to Tawfik Tirawi, the head of the Palestinian committee investigating the death and one of those who was holed up with Arafat in the Muqata under Israeli siege for more than two years, there will be no cameras to record the event. "Due to the particular situation, there will probably be no media coverage. It's very difficult to allow journalists to be around because of all the difficulties of the operation," he told the Guardian.

Tirawi has requested details of the French investigating magistrates' requirements in order to iron out any objections. But the Palestinian leadership has stated its willingness in principle to co-operate with the murder inquiry, launched last month at the request of Arafat's widow, Suha, a French citizen. Her move followed a claim in July, broadcast by al-Jazeera, by a Swiss laboratory that it had detected the presence of a deadly radioactive substance, polonium-210, on Arafat's personal effects.

Despite having refused permission for an autopsy on Arafat's body, last year Suha handed over items including a toothbrush and underwear to scientists at the Institute of Radiation Physics in Lausanne.

"We measured an unexplained, elevated amount of unsupported polonium-210 in the belongings of Mr Arafat that contained stains of biological fluids," François Bochud, the institute's director, told al-Jazeera. Saying tests on Arafat's corpse were required to confirm the findings, Bochud added: "We have to do it quite fast because polonium is decaying, so if we wait for too long, any possible proof will disappear."

Polonium, the substance linked to the death of the former Russian spy Alexander Litvinenko in 2006, depletes rapidly in bones and soft tissue. The institute has estimated a 50% chance of finding traces in samples from Arafat's body.

The al-Jazeera claims reignited suspicions long held among Palestinians that Arafat had been a victim of foul play – the work of Israel's fabled intelligence agency, Mossad, the architect of the deaths of many of the Jewish state's enemies. "Yasser Arafat was assassinated by Israel – all Palestinians know that," said Samer Karaka, minding a shop opposite the Muqata a few days ago. But he was sceptical that the new investigation would produce proof. "Israel will not allow it," he shrugged.

The new claims also stirred old animosity between Suha Arafat and the Palestinian Authority. She pointedly asked the PA "to suspend all initiatives", saying the French investigation "should take precedence over all other procedures, because it is the incontestable guarantee of independence and neutrality". Her statement suggested a lack of faith in the PA to conduct a credible inquiry, despite its re-establishment of an investigations committee in 2010. Ms Arafat's involvement with al-Jazeera – another bete noire of the PA following its disclosure last year, along with the Guardian, of the Palestine papers detailing peace negotiations with Israel – also rankled with Palestinian officials.

Ms Arafat was not popular among Palestinians. Many were sceptical about her conversion from Christianity to Islam, resented her affluent lifestyle and harboured suspicions about how it was funded. While Arafat was besieged in Ramallah, his wife lived in comfort in Tunis.

For the two and a half years before his death, Arafat was a virtual prisoner inside the ruins of his presidential compound. Israeli tanks and bulldozers had reduced much of the Muqata to rubble during the second intifada, the Palestinian uprising from 2000-05. Arafat feared that if he left the compound, Israeli forces would finish the job – and quite possibly assassinate him. His fears were not unfounded. In September 2003, the then Israeli deputy prime minister, Ehud Olmert, said in a radio interview: "Expulsion is certainly one of the options. Killing is also one of the options."

Life inside the Muqata was not conducive to good health. "The living conditions in the last days were very difficult," said Tirawi. "Sometimes there was not enough oxygen. Sometimes there was not enough clean water. We were completely surrounded. The health of all the people in the Muqata was suffering."

About 270 people were confined inside the compound, including Arafat's close aides, security guards and dozens of Palestinian militants wanted by Israel. "Imagine – 270 people living in such a small space. People were sleeping over each other," Tirawi recalled.

Arafat's private quarters comprised a small, windowless room with a narrow camp bed. According to Tirawi, who was then the Palestinian intelligence chief, the leader preferred to sleep alongside his cohorts. Accustomed to travelling the world to meet heads of state and political leaders, Arafat found his isolation dispiriting. "No one from the outside world would call him," said Tirawi, claiming that US pressure was the reason.

Supplies of food, drinking water and other essentials passed through Israeli hands on their way to the Muqata, he said. "The Israelis would take everything for one or two hours, and then let it come in." The diet was meagre but healthy: chicken, fish, honey, vegetables.

But in mid-October 2004, Arafat fell ill, with vomiting, diarrhoea, stomach pains and fever. Doctors were summoned but his condition worsened. Vivid red patches appeared on his cheeks and his weight loss accelerated. "He knew he was sick, but he would say, 'It's nothing,'" recalled Tirawi.

Arafat needed urgent and sophisticated medical treatment, beyond the facilities available in Ramallah. Eventually senior officials sought – and received – assurances from the Israeli government that if the president left the Muqata, he would be allowed to return.

Visibly frail, and with an unfamiliar woollen beanie in place of his trademark chequered keffiyeh, Arafat was flown to a military hospital in Paris on 29 October. Less than two weeks later, he was dead.

A medical report by French doctors who attended Arafat concluded that he had a stroke after suffering from a blood disorder known as disseminated intravascular coagulation. But rumours of poison soon began to circulate. Last month, Dov Weisglass, an aide to the then Israeli prime minister Ariel Sharon, rejected allegations of foul play. While acknowledging Arafat as "one of Israel's worst enemies", he told Army Radio: "Israel did not have any hand in this." Another senior Sharon aide, Raanan Gissin, told the Associated Press that Israel "never touched a hair on his head".

According to Tirawi, two Muqata residents died of unknown causes soon after Arafat's death. "We need to know why they died too." He would not be drawn on the polonium issue – "I cannot pre-empt the investigation" – but if Arafat was poisoned, Tirawi conceded, it must have been with inside help, as Israeli agents outside the Muqata would have had no idea which food was destined to be consumed by Arafat.

"Some days we would get 100 chickens delivered. If someone put polonium or any sort of poison in his food, it must have been a Palestinian. Maybe – maybe – there was inside collaboration."

In the past, Tirawi has expressed scepticism over claims that Arafat's food or water was poisoned. But, he insists, Israel's siege of the Muqata contributed to Arafat's death. "Regardless of how, of the way it happened, the Israelis killed Yasser Arafat. The situation that was around him, the living conditions. But it's not an easy task to get at the truth. There's a chance we might never know."