During the final week of the 88th Tour de France in July 2001, a 28-year-old American rider called Jonathan Vaughters was riding with some team-mates during the rest day in Pau, when a wasp became trapped in his sunglasses. Vaughters was allergic to stings and when he returned to the team hotel, his eye was the size of a golf ball. "The only thing that's going to reduce that swelling is a cortisone injection but if you take it you'll test positive," his team doctor told him.

Vaughters was distraught. "But that's ridiculous … I can't see! I can't ride my bike! How will I finish the race?" he said. "I'm sorry Jonathan," the doctor replied. "There are no exemptions for allergies. We have to do this by the book."

"I understand," Vaughters conceded, "but I'm not going to abandon. We'll see how it is in the morning."

The swelling did not recede and the following morning Vaughters stepped from the team bus in Pau looking like the Elephant Man. His Tour was effectively over, but as a gesture to highlight the absurdity of the doping laws, he had decided to line up for the start and climb off his bike as soon as the flag dropped.

As he was making his way to the start line he crossed paths with the race leader, Lance Armstrong. Two years previously, during Armstrong's first Tour win in 1999, they had been team-mates at US Postal, but Vaughters had not enjoyed the experience. The win had been fuelled by doping and Vaughters had left at the end of the season and found a much saner working environment with the French team, Crédit Agricole.

Armstrong did not disguise his contempt. "Poor Jonathan and his stupid little French team," he spat. "What the fuck are you like? If you had stayed with me, this would have been taken care of but now you are not going to finish the Tour de France because of a wasp sting."

Vaughters was distraught. "I thought: 'Fuck! Here I am, on this team that is really trying to stick by the books and this guy is making fun of us for playing by the rules. That was the moment that effectively ended my career," he says. "I didn't want to race any more. It just didn't seem to matter to me after that."

Armstrong liked to boast about his friends in high places and those friends had served him well. During that first Tour win in 1999, he should have been disqualified after testing positive for a corticosteroid but was saved by a backdated therapeutic exemption. In 2002, Floyd Landis says that Armstrong told him that another positive test at the 2001 Tour of Switzerland had been overturned.

For Landis, who would succeed Armstrong on the list of Tour winners three years later, it was the pivotal moment in his decision to dope. "That was all of it," Landis says. "If I had any reason to believe that the people running the sport really want to fix it, I may have actually said: 'If I wait long enough I'll have the chance to win without doing this [doping]', but there was no scenario in my mind where in my lifetime I was going to get a chance to race the Tour and win clean."

Since Tommy Simpson's death in 1967, 86% of Tour de France winners have been tarnished or implicated by doping. What's wrong with this sport? Why does it keep happening? As Armstrong is confined to history, it's his relationship with the International Cycling Union (UCI) – he made donations to the sport's governing body while competing – that disturbs most.

Why have they been bending over backwards this last month to wrestle his case from the US Anti-Doping Agency? Why wasn't Armstrong sanctioned in 1999? What happened at the 2001 Tour of Switzerland? Why were Floyd Landis's claims about doping at US Postal never investigated? Why are the UCI suing journalists who have asked these questions?

Do we have any reason to believe that the people running the sport really want to fix it? The jury is out.