• Slovakian wins his third 2018 Tour de France stage in Valence • Flare thrown into peloton despite Tour director’s appeal to fans

Christian Prudhomme’s appeal for calm before Friday’s 13th stage fell on deaf ears when a lit flare was lobbed into the peloton a few hours later.

The flare was thrown from the side of the road towards the end of the stage – which was won by Peter Sagan in a sprint finish – and added weight to the warning sounded by the Tour de France director.

Prudhomme had spoken out after tensions increased during Thursday’s chaotic climb of Alpe d’Huez in which Chris Froome was jostled and spat at, and his rival and former Tour de France champion Vincenzo Nibali was forced out of the race after crashing because of a spectator.

“We need to restore calm and respect all the riders,” Prudhomme said. “It was a very annoying climb of Alpe d’Huez. The riders on the Tour, and champions of the Tour, must be respected, as they are by the large majority of the public.

“It was very calm for 10 days, with only a few anti-Froome or anti-Sky placards, but at a stroke, it all went up again.”

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The cumulative effect of serial doping scandals, from the Festina Affair to Lance Armstrong, is that there is less respect for the Tour peloton now than 20 years ago. Meanwhile, the knives that have been out for Froome and Team Sky since the Grand Départ in the Vendée are now being sharpened.

The 13th stage , from Bourg d’Oisans to Valence, raced by a peloton shorn of many big-name sprinters, was won with a degree of inevitability by Sagan but the day’s events were overshadowed by the aftermath of the chaos on Alpe d’Huez.

Nibali was forced to leave the Tour following his crash. The 2014 champion, chasing Froome through a pall of smoke caused by roadside flares, was brought down by a strap hanging over the barriers from a spectator’s camera.

After a 120km round trip from Alpe d’Huez to a Grenoble hospital where his fractured vertebrae were confirmed, Nibali was visited late on Thursday night at his hotel by an apologetic Prudhomme. The Italian is likely to return to racing at the Vuelta a España, while his team, although angered by his crash, are not expected to take any further action.

“It’s a paradox that Vincenzo Nibali, who has nothing to do with Team Sky, ended up on the tarmac,” Prudhomme said.

Facebook Twitter Pinterest Steven Kruijswijk struggles through big crowds and flare smoke on the ascent of l’Alpe d’Huez on Thursday. Photograph: Philippe Lopez/AFP/Getty Images

Asked about that incident and about his own treatment by spectators, Froome was critical. “During the race, it’s the responsibility of the organisers to protect the riders,” Froome said.

Although Team Sky’s principal, Dave Brailsford, said “you expect professional athletes to play and entertain without being impacted on by the crowd”, the team’s head of technical operations, Carsten Jeppesen, told the Guardian that rider security on Alpe d’Huez had actually been improved.

“They have done a lot more than usual,” Jeppesen said of the race organisers, ASO. “I think they’ve done a really good job actually. ASO takes it seriously and they are trying to bring in more cops and make sure that certain key points are taken care of.

“Luckily Chris was not knocked off by the guy that pushed him, but it’s Alpe d’Huez. It’s not the first time something like that happened there. It is one of the iconic places in the sport and there was also a lot of British fans out there and a lot of support.”

Despite that, Froome and Thomas were booed yet again at Friday’s start although it is clear the reigning champion is seen as the villain of the piece.

The French media, now expecting a sixth Team Sky win in seven years, have also picked up the baton. Team Sky was described as the “snake with two heads” by Liberation, while L’Equipe said that “when you wear the jersey of the British team, suspicion is as contagious as herpes”.

The physicality of Thomas’s strength to sprint clear of his peers at the top of the exhausting climb to Alpe d’Huez, brought comparisons with Eddy Merckx from one veteran in the press room. But it also brought eye-rolling and derision from others, baffled by Sky’s continuing production line of Grand Tour contenders.

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“If my grandma rode for Sky she could win the Tour,” a fan named as Jules told L’Equipe after he had booed and jeered Thomas’s success on the Alpe.

Meanwhile, some believe that Thomas is merely Froome’s stooge, a glorified lead-out man, there to take the sting out of the world time trial champion, Tom Dumoulin, before the final and potentially decisive time trial next Saturday to Espelette.

But what if Thomas is the one bluffing? What if Sky harbour doubts about Froome’s capacity, after his win in the Giro d’Italia, to rise to the challenge of winning his fourth Grand Tour in a row, a feat which, incredibly, would equate to being unbeaten for three whole months of racing?

What if, rather than being simply a decoy for the under-fire Froome, jeered and jostled from the Vendée to Valence, it was always all about Thomas, and enabling him to profit from Dumoulin’s focus on marking Froome? In Team Sky’s long history of befuddling cycling’s establishment with doublethink and contradiction, that might yet be the greatest coup of them all.