Now the man they hoped would save the Tour faces a new inquiry into doping allegations

That prospect would be a catastrophe both for cycling and for the organisers of the Tour de France, who had hoped the man wearing the yellow jersey on today's final sprint down the Champs-Élysées would help to redeem an event that has seemingly been heading for oblivion.

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Sadly for those hopes, The Mail on Sunday can reveal that Dick Pound, the chairman of the World Anti-Doping Agency, is to pursue further investigations into evidence that appears to link Contador to doping and which could yet see the yellow jersey stained beyond redemption.

A race which started amid optimism and sunshine, with millions cheering on the streets of London and the roads of Kent three weeks ago, will end engulfed in fears that the credibility of the sport and the race can never recover.

When last year's victor,Floyd Landis,rode into Paris in glory only to be disgraced days later by a positive testosterone test — a result the American is still contesting — it appeared the Tour had reached its nadir. But this year there has been no relief from the scandal of doping.

Contador, 24 and from Madrid, retained the leader's yellow jersey after finishing fifth in yesterday's time trial, which was won by his Discovery Channel team-mate, American Levi Leipheimer. But Contador's likely triumph today will have come about only because of leader Michael Rasmussen's forced retirement from the race on Wednesday when the Dane's team, Rabobank, sacked him after incessant media pressure over missed tests and allegations that he had asked a friend to smuggle doping products.

The expulsion of Rasmussen has been accompanied by the dope-test failures of Patrik Sinkewitz,Alexandre Vinokourov and Cristian Moreni and the withdrawal of the Astana and Cofidis teams. German state TV stopped covering the race and a string of sponsors — Cofidis, T-Mobile,Rabobank, Fondital, Skoda, adidas — are questioning their future involvement in the sport.

Now Contador faces investigation for a past connection to Eufemiano Fuentes, one of the most prolific doping doctors in history.Dr Fuentes was arrested last year at the beginning of Spain's biggest doping scandal, codenamed Operation Puerto. Spain's Guardia Civil uncovered evidence of systematic doping practised by Dr Fuentes with several cyclists and the revelations have accounted for some of the biggest names in the sport, including Jan Ullrich and Ivan Basso. Contador escaped even though he rode for the team at the centre of the scandal, Liberty Seguros. While some documents appeared to link him to Fuentes, his name was not on the list of cyclists being investigated by the Spanish judicial authorities last year and last March, the judge in charge, Antonio Serrano, dropped the case against all suspects, claiming that he could not be sure that Spanish health laws had been breached.

However, Pound said: "This investigation may have gone away in Spain but we are currently working with the UCI on going through 6,000 pages of documentation gathered from the Operation Puerto investigation."

Documents seized at the home of Dr Fuentes by the Guardia Civil are also being studied by German prosecutors, who are weighing up whether they can bring cases of fraudulent behaviour against a number of German nationals involved in the case.

If WADA or the German state authorities uncover new evidence that links Contador to doping, then Pound will pressurise the UCI to bring a doping charge against him. Crucial to Pound's inquiries will be a document written in Spanish in what appears to be the handwriting of Dr Fuentes. It describes what is alleged to be individual doping plans for Liberty Seguros riders in 2005,when Contador was a member of the team. For example, under the initials RH, understood to refer to the disgraced Spanish cyclist, Roberto Heras, numbers appear under the headings I-2, I-3 and TGN. The latter is claimed to be a reference to a banned growth hormone, while it is believed that I-2 and I-3 refer to banned insulin growth factor.

The initials of what appear to be all members of the Liberty Seguros team are listed, including one identified as 'AC'. The programme for AC is listed,in Spanish, as 'nothing or the same as JJ'. And JJ's plans for 2005 were to 'always have I-2'.

It is, of course, possible that AC was given 'nothing' throughout his programme and so breached no rules. But Professor Werner Franke, a hugely respected anti-doping expert who has advised the German authorities in their current investigations and who is familiar with the Operation Puerto documents, said: "The team had different programmes at different times. So at certain times AC had to be given the same programme as JJ — and at other times he was to be given nothing."

The JJ mentioned in the documents is now known to have been Jörg Jaksche,the German cyclist who has admitted doping since 1997, including his two years at Liberty Seguros in 2005 and 2006.

The Mail on Sunday understands that last Wednesday and Thursday Jaksche met German state prosecutors in Ansbach, Bavaria, and spent two days detailing his offences. His motive is partly to soothe his conscience but also to strike a deal with Pound,and it is this revelation which may cause problems for Contador.

WADA rules allow for the reduction of doping bans if athletes co-operate in exposing doping cartels and sources close to Jaksche say he will tell the authorities, both sporting or judicial, everything.

Pound has confirmed that last month he was contacted by an intermediary representing a German cyclist, who wanted to discover whether he would have the chance of a reduced ban if he provided information on doping.

"I was approached to find out whether there is this rule and I confirmed that there was," said Pound.

"But I told them that it would only apply depending on the extent of any confession.We would have to be satisfied that it was a full and complete one."

Jaksche has already been frank about his own doping in the pages of the German magazine Der Spiegel, explaining how he injected EPO, took cortisone and allowed blood transfusions to be performed in an attempt to keep his contracts and improve his cycling.

But he was encouraged by his advisers also to speak to the German authorities, to prove to Pound that this was more than a media stunt and that his commitment to come clean was sincere. And it is his ability to shed light on the doping programme of AC that now makes him a potentially valuable witness in the future of cycling.

Pound says that he does not yet know the name of his potential informant, but The Mail on Sunday has been told by a reliable source that it is Jaksche. Pound now wants to interview him in Montreal, Canada, to see whether he might be considered for a shortened ban.

"He would have to come and agree to be interviewed by us," said Pound. "We would have to form an independent judgment on whether it was a full and complete confession."

Asked whether he would quiz Jaksche on the doping programme of AC, Pound said: "I would expect we would ask him about this."

Contador has been cleared by the Spanish judiciary, who could find no evidence to link him to doping.

Enrico Carpani, the spokesman for the governing body of cycling, the UCI, has also confirmed to The Mail on Sunday that Contador had been cleared to ride by them after they had examined the documents provided by the Guardia Civil.

The Spaniard has never failed a drugs test and has repeatedly declared himself to be a clean rider. "If I wasn't, I wouldn't be here," he said after taking over the race lead from Rasmussen.

Questioned about his links to Fuentes, he said: "My implication in Operation Puerto has been explained by the UCI. I was simply in the wrong team at the wrong time but I have already made it clear that I had no connection to the doping plot that is being investigated.' But Contador will be missing at least one fan as he launches the victory sprint down the most famous street in France.

"I certainly wouldn't go to watch the final stage of the Tour and I won't be watching it on TV," says Pound. "It may be called the Tour de France, but until the credibility of the race can be restored, it's not the Tour de France."