Time will tell, and it may take years for science to finally establish the detail of what we have witnessed in the past three weeks, but for now we should enjoy Chris Froome's victory in the 100th Tour de France.

Instinct suggests that Froome is an honourable character, an intelligent athlete who stares you in the eye and says unblinking: "I'm not cheating." Of course, we have been lied to before, but Froome's demeanour is light years away from that of the bad old days of Lance Armstrong and his bullying cronies.

Yet many here in France are convinced that he is just another fraud, a conclusion he reluctantly accepts. "It's 100% understandable given where the sport has come from," he said. "I think whoever wore the yellow jersey was going to come under the same amount of scrutiny, the same amount of criticism."

Fair enough and true. The problem is that recent history also suggests it is difficult to win the Tour de France without recourse to the medicine cabinet. Caught in the middle, then, between the sceptics and the believers, is this wafer-thin expatriated Briton, who protests his innocence with clipped, modulated vowels and a shy manner.

"I completely understand that scepticism as I am also one of those who have been let down by the sport," Froome said last night, after finishing third on the penultimate stage from Annecy to Annecy-Semnoz, behind Colmbian Nairo Quintana and Spain's Joaquim Rodriguez.

"I just hope that through winning this year's Tour I can help change that. I know it's going to take a lot more time, but we're willing to try to do everything it takes to show people that the sport has turned around."

Froome heads for the Champs-Elysees today with a lead of 5:03 and his journey to Tour glory – via Kenya, South Africa, Monaco and London 2012 – has been a remarkable one.

"When I think that I started riding on a little mountain bike in Nairobi, to being here in yellow at the Tour de France, it's difficult for me to put into words. It's been an amazing journey," he said.

Nor has it been the overnight success many believe it to be, as Froome has been on the verge of winning one of Europe's big three national tours since 2011, when he placed second overall in the Tour of Spain.

"The first time I thought I could realistically become a contender in races like the Tour de France was during the 2011 Vuelta a Espana," the Team Sky rider said. "Until then I found it very difficult to keep my performances consistently high throughout a stage race."

In that year's Vuelta, Froome climbed with the best, as he rode in support of Bradley Wiggins. He said: "That gave me a lot of confidence and belief in myself that I actually did belong in the group of riders at the front."

He is certainly a phenomenon, yet there remains something freakish about Froome. His slight frame and frenetic pedalling style when attacking have baffled French audiences, who have been largely left cold by the new champion.

His team have, under intense media pressure, released a significant amount of information about his power outputs and physiology. He has been cross- examined, tested, and cross-examined again, but it's not enough to quieten the cynics.

But it's also worth remembering that if Froome was such a Machiavellian character he might have won no less than three Grand Tours by now, last year's Tour de France and the 2011 Vuelta, in which he subjugated his ambitions in support of Wiggins. At the moment there is no evidence against him beyond a whispering campaign, a sound drubbing of his rivals and some bad science in a French national newspaper that detests the Tour. That's certainly not enough to condemn him, as some already have.

Yet this is what happens when a sport breaks down, when the drug tests can't be trusted, when corruption becomes all-pervading. Cycling had a substance problem and this year's Tour has demonstrated it's still emerging from rehab.

Froome will continue to be doubted by the sceptics, but the Tour could do worse for a new champion. Victory for Alberto Contador for example, touted as Froome's biggest rival before the race began, who threatened to skulk in his hotel room after being asked doping questions in one mid-race press conference, would have been a PR disaster.

For now there has been no messages of congratulations from Wiggins, which probably tells you all you need to now about his deteriorated relationship with Froome. The latter showed the merest flicker of disappointment at the snub, but he need not worry. The leadership debate at Team Sky has been emphatically resolved. The question now is how many more Tours de France can Chris Froome win?