PAU, France >> As the start of the Tour de France loomed this month, Chris Froome, the four-time champion, was still under investigation after testing positive during last year’s Vuelta a España for an excessive amount of an asthma medication, which he is allowed to use at certain levels under a doctor’s prescription.

He was cleared to race, however, when the International Cycling Union dropped its investigation and the World Anti-Doping Agency concurred. But that may have been the last bit of unalloyed good news Froome has received.

On today, the final mountain stage of the Tour delivered the verdict that Froome, who was born in Kenya but who races as a Briton, would not add another Tour victory this year. As was the case in another Pyrenees stage earlier this week, the rider who once was untouchable in the mountains faded dramatically toward the end of the day’s racing.

Froome was also bounced off the podium, pending the results of Saturday’s time trial, in the 120-mile (200-kilometer) stage today won by Primoz Roglic, a Slovene who rides for the LottoNL-Jumbo team. Geraint Thomas, who entered the race as one of Froome’s assistants on Team Sky, maintained his hold on the yellow race leader’s jersey with Tom Dumoulin of the Netherlands in second.

This year’s Tour was sour almost from the beginning for Froome. Jeers have followed him along the route, and signs attacking Team Sky have popped up. In the most extreme cases, spectators have spat on Froome and his teammates, doused them with liquids and tried to punch them.

In a sport with a long history of doping scandals, many fans concluded that Froome had escaped punishment because of his status within the sport and the costly legal defense provided by his team.

Many have come to the conclusion that the situation has become a mess not just for Froome, but for the public’s faith in the anti-doping system.

“Given WADA’s conflicted leadership and lack of oversight, it’s pretty simple why people are skeptical when a star athlete walks,” said Travis T. Tygart, chief executive of the U.S. Anti-Doping Agency.

“What’s even more unfortunate is that this may be exactly what should have happened given the facts of the case,” Tygart said. “But now an athlete is unfairly and publicly questioned without the details to show the decision was the right one for justice.”

WADA said in a statement: “In leading the fight against doping in sport, WADA is sometimes forced to make difficult decisions related to complex cases that people, who are not in possession of the facts, do not understand or agree with. This is one of those occasions.”

The organization added, “WADA is convinced that, in view of the complex and unique circumstances of Mr. Froome’s case, the UCI reached a correct and fair outcome.”

Until Froome fell apart at the end of Wednesday’s stage, it had been assumed that Thomas was merely the caretaker for the yellow jersey, which he first pulled on July 18. It had been expected that Froome would take it over, perhaps today, then add to his margin in Saturday’s race against the clock.

Thomas’ overall victory now hinges on the time trial. Dumoulin, a Dutch rider, is an expert at the event and a former world champion in the discipline. But at 32 kilometers (20 miles), the race may not be long enough for him to overcome Thomas’ advantage of 2 minutes 5 seconds.

Still, Thomas was reluctant to declare himself the winner.

“It’s obviously getting closer, but we have one more day,” he told reporters today. “I need to do a really good TT now,” he continued, referring to the time trial. “I have a nice advantage, but I still have to be on the ball.”

While it was not to be at the Tour, Froome has managed spectacular comebacks before. In May, he came out of nowhere to win the Giro d’Italia in its closing phase. (The drama of that comeback also helped fuel skepticism about Froome among fans who have seen too many spectacular performances that proved to be the results of doping.)

The disappointing Tour de France for Froome, and the suspicion surrounding him, come on an anniversary the Tour organizers are doing their best to forget. Twenty years ago, French police stopped Willy Voet, a trainer with the French Festina team, as he crossed the border from Belgium in a car that was virtually a mobile pharmacy. The series of raids and arrests that followed nearly brought that year’s Tour to a premature close, and in some ways set up Lance Armstrong’s postcancer return a year later — which was portrayed as a fresh start for the Tour — and all the scandal that eventually flowed from Armstrong’s dominance and doping.

It says something about the state of cycling that there is still a role for a group known as the Movement for Credible Cycling. In 1988, Roger Legeay, the group’s president and founder, was the head of the French GAN team, a direct descendant of the Peugeot team that was long considered cycling’s version of the New York Yankees.

Sky conspicuously does not belong to Legeay’s group, unlike seven of the 18 World Tour teams. But if Sky had been among its members, the group’s rules would have required it to voluntarily suspend Froome until the cycling union released its decision.