The average speed around the 250m track was approaching 40mph. The temperature was 28C, precisely calculated to help muscles stay relaxed. The athletes looked like ball bearings flung around the velodrome’s cauldron. It was midway through the men’s team pursuit final at this year’s Olympic Games in Rio de Janeiro and Great Britain’s cyclists were in trouble.

“The problem was that the Australians set off at such a ridiculously fast pace that by the time we got to the 3km mark, both teams were three seconds up on the world record,” says Ed Clancy, one of the British team. At halfway, Australia were more than a second ahead, a huge gulf by track-cycling standards. Then, bafflingly, thrillingly, the British appeared to find a turn of speed. They closed the gap. Then they took the lead. They won in three minutes and 50.265 seconds, breaking the world record they had set just a few hours earlier during qualification.

The final kilometre was an illusion, says Clancy. The Brits had actually begun to decelerate. The Australians were spent, slowing down even further. “Both teams exploded,” he says. “It’s just that we held it together a little bit better than those guys.”

Holding it together has become the hallmark of British Cycling, the Manchester-based organisation that runs elite riding in the UK and whose athletes have dominated the medal table in the last three Olympics. In 2004, Clancy became part of the first intake in its academy programme, designed to find promising young riders and shape them for elite competition. This system has forged champions such as Mark Cavendish, Geraint Thomas and Lizzie Armitstead.

Today Clancy is a triple Olympic champion and one of a group of British cyclists to have reigned over three consecutive Games. At Beijing in 2008, they brought home 14 medals, including eight golds. At London in 2012, they won 12 medals with eight golds. Then, in Rio, Team GB grabbed 12 cycling medals with six golds, twice as many as any other nation. These victories were the foundation of the country’s remarkable second-place finish in the overall medal table, Britain’s best Olympic performance in more than a century.

Track cyclist Jack Carlin at the National Cycling Centre velodrome © Nadav Kander

Thanks to this record, British Cycling has been dubbed the “medal factory”, a conveyor belt of talent created by Sir Dave Brailsford, its former performance director. Before his appointment in 2003, British Cycling had managed only one gold medal since the organisation’s founding in 1959. Brailsford changed that with his doctrine of the “aggregation of marginal gains”, a maniacal search for small improvements in performance that add up to a decisive advantage. Based on the Japanese business theory of kaizen, this approach had previously influenced companies such as Toyota, Ford and Lockheed Martin. Brailsford adapted it for sport and has since advised the civil service on how to improve processes in the National Health Service.

Clancy arrived at British Cycling aged 18, “pretty old” by his estimation, giving up a university place for a £3,000 annual stipend, free board and the chance to ride bikes. Back then, fast times were emphasised less than simply working hard. Clancy remembers Rod Ellingworth, the academy’s founding coach, arriving before 7am at the house in which young riders lodged. Ellingworth insisted they pedal to headquarters several miles away, regardless of the weather. “Rod was adamant he wanted to see character,” says Clancy. “He didn’t just want to see talent. He wanted to see riders that worked for it.”

Fifteen years later, this discipline pulled Clancy through in Rio. “When you’re under that much pressure, you’re changing the game on the spot, you’ve still got to keep in the back of your mind that you’re not just going down the straight, zigzagging around,” he says. “That’s all ingrained in our brains from doing it time and time and time and time again. That’s what Rod was thinking about all those years ago.”

The medal factory itself is based at the unassuming National Cycling Centre, which opened in 1994. From the outside, the building looks little more than a plush leisure centre. But beyond the white walls and glass doors lies a cyclist’s paradise. The centre has a velodrome and track made of Siberian pine wood, judged to be the best possible material for racing on. Within its bowels is a competition-ready BMX arena, fully covered for year-round use and the only such indoor track in western Europe. Nearby, 12km of outdoor mountain-biking trails snake around the site of a former coalmine.

The National Cycling Centre has a competition-ready BMX track arena, which is fully covered for year-round use. Grid design © Nadav Kander

Inside, both physical and technological gains are pushed on a daily basis. In 2004, British Cycling created the “Secret Squirrel Club”, a group that develops technological advances only released on the eve of a Games. In Rio, Clancy was handed a £10,000 Cervélo T5GB bike painted with extra-smooth resin developed by Formula One teams to be ultra-aerodynamic. These innovations are hidden away in a secretive bunker dubbed “Room X”, which only a chosen few are able to enter.

The organisation is dedicated to doing an ever-better job at generating winners. Over the past two years, it has developed a new data-driven system, known internally as the “Readiness Index” (RI), that aims to reveal if a rider is on track for Olympic glory. Andy Harrison is British Cycling’s programmes director and interim head: an intense man who rarely blinks behind thick-rimmed glasses, he speaks in numbers and management jargon. A nation can win a maximum of 34 cycling medals at a Games, he says. It may be impossible to win the lot but the RI is an attempt to get closer. “This is not marginal gains,” he insists. “This is new. This is how we get a dynasty.”

Since Rio, I have spoken to many British Cycling executives, coaches, riders and others close to the organisation. They may dress in pristine Team GB tracksuits but, in their precision and approach, they evoke scientists in white coats. They describe a system that is forward-thinking, clinical, even brutal.

Yet, as these conversations unfolded, it appeared that British Cycling’s grand ambitions could be derailed. It faces investigations over allegations of bullying and doping. Key leaders have left. Sports science is being overshadowed by scandal. The group says it has created a blueprint to triumph at the 2020 games in Tokyo and beyond, but there are fears among others that the medal factory is breaking down.

Joe Truman was four when he learnt how to ride a bike in a field in Petersfield, Hampshire. But he soon ditched cycling for football. A decade later, the teenager began to join his father on weekend rides, then started competing in local races. In 2011, he applied to the British Cycling’s “talent team”, an under-15s apprentice programme, and was selected. Youngsters spent their holidays at weeks-long boot camps, on bikes for several hours a day.

Academy rider Joe Truman © Nadav Kander © Nadav Kander

“You get the impression it might crack some people,” says Truman. “You’re in a youth hostel with eight other lads. It’s cold. Unless you enjoy the sport, you won’t be able to cope.” Truman did, though, and progressed to the junior academy for those aged 15 to 17. Here, cyclists are told of their mission. “I remember having a meeting when we started, and a photo of Tokyo flashed up. They had worked out the percentages on average of the people in this room who would be there . . . It was making it clear, even back then, that the goal is Tokyo.”

All I have to do is get faster and faster. There’s a process to it

British Cycling has a Darwinian selection regime. Every year the track cycling “pyramid” begins with about 70 riders trained as apprentices. Around 16 make the academy programme. Eight will join the “Olympic podium” squad in preparation for the Games. From the original group, one athlete on average will win a gold medal.

Truman, now aged 19, is a senior academy rider, one tier below the “podium” team, and is seeking a place on the men’s sprint squad. To do so, he needs to edge out one of the current line-up. That will be tough. The British team of Jason Kenny, Callum Skinner and Philip Hindes smashed the Olympic record in Rio. By 2020, when Truman will be 23, if he can’t break into the sprint team, he could be cut from the programme altogether.

Academy rider Ellie Dickinson won a gold medal at the track world cup in Glasgow this month © Nadav Kander

Truman is not fazed. “I wouldn’t say it keeps me up at night because, at the end of the day, all I have to do is get faster and faster,” he says. “There’s a process to it. If I meet that process, I’ll go faster. If I go faster, I’ll get in the team.”

Until the 1990s, British Cycling was an international laughing stock. Mark Ingham, a mechanic at the organisation, recalls riders being told to return their jerseys at the end of competitions so they could be reused. That changed in 1997 when Prime Minister John Major decided to redirect National Lottery money to elite athletes in response to the country’s abysmal showing at the Atlanta Games in 1996.

After Brailsford took charge in 2003, a system was built that prepared riders to peak at the Olympics. Sporting regimes in other countries base funding decisions on results at annual competitions. UK Sport bases funding on the chances of winning Olympic medals. British Cycling, which received £30m in the four years up to Rio, is one of the best-funded Olympic programmes in the country, if not the world. “The way I see it is it’s like a business,” says Clancy. “It’s a business funded on the Olympic Games.”

Given the financial incentives, British Cycling wants to guarantee wins. In April 2014, it began a “market analysis”, collating information on its own riders and rivals. These data are the basis of the Readiness Index. “We try to forecast and predict what it looks like in the future and work back from that in a timeline,” says Ian Yates, performance pathway manager and one of the creators of the system.

Ian Yates, performance pathway manager and one of the creators of British Cycling’s Readiness Index © Nadav Kander

British Cycling employs 28 coaches, 20 of whom are dedicated to younger “pathway” riders. They feed the index by creating in-depth profiles of each cyclist, logging physiological changes, such as improvements in strength; performance indicators, such as increases in speed and finish times; and qualities that are harder to quantify, like whether riders show “grit”, “relish a battle” and “bounce back after setbacks”. This information produces a “playbook” for riders; specific targets to hit from pedalling power to muscle size.

Every three months, British Cycling assesses each rider. Anyone not en route to a medal faces being cut. Yates says the data don’t just act as a selection tool but also as a motivational device. “Millennials crave a lot more buy-in,” says Yates. “If you go back 10 or 12 years, that cohort of young people were quite happy to be told what to do and would do it. And now, they ask, ‘Why do I need to do this?’” The organisation has gathered the answers to these questions. Or as Truman says, he knows the process to getting faster.

The data-driven approach also suggests that British Cycling lacks enough female riders to be sure of sprinting medals in 2020 and 2024. Alongside UK Sport, it has initiated a “Talent ID” programme, scouting for 15- to 16-year-old girls. Olympic champions such as Laura Trott and Victoria Pendleton, now household names, were found through similar searches. “We are in the fantastic and fortunate position that we don’t have to convince too many people,” said Kevin Stewart, the academy sprint coach. “There’s people banging on the door. There’s people emailing us all the time.” Over the past few months, more than 2,200 girls have been tested. Only one or two will be selected.

World under-23 cyclo-cross champion Evie Richards © Nadav Kander

Evie Richards was spotted four years ago. Then 15, she was trialling with the England women’s hockey team and, to keep up her fitness, began joining her father on mountain-bike rides around the Malvern Hills. At her dad’s encouragement, she began entering major junior races despite being a novice. “I was going quite quick but I was running down all the [wrong] lines,” she says. Despite her technical deficiencies, she kept beating the opposition. “I came out of nowhere on a rubbish bike,” she says. “I don’t think anyone was expecting it.”

I came out of nowhere on a rubbish bike. No one was expecting it

Simon Watts, British Cycling’s mountain-bike academy coach, spotted her training at a local club. As well as being physically impressive, Richards was exhibiting “coachability”. “It was the aggression she was putting into the tasks that she was being set,” he says. “She was physically finishing them extremely drained, so she was going very deep in her efforts. She was making technical mistakes and, through language, she was self-punishing herself and considering what she had done wrong. She was then repeating it to try and get it better rather than losing concentration.”

Richards joined the academy and was soon thrown into the British team for international events. In January, she entered the under-23 cyclo-cross world championships at Zolder, Belgium. The race took place in torrential rain, with cyclists forced to pedal up steep slopes on wooded hills.

Simon Watts, academy mountain-bike coach at British Cycling © Nadav Kander

In person, Richards speaks through a smile. But footage from the event shows her face screwed up in concentration, startling rivals with her racing attacks. “I was completely blanked out,” she says. “There is no expression. I was in such a zone.” As she turned the final corner, face and jersey sprayed with mud, Richards peered over her shoulder. Realising no challenger was in sight, the smile returned. She was a world champion, aged 19.

Richards could form a crucial part in the British Cycling jigsaw. Brits have ruled track cycling but have a patchy record in other riding disciplines. According to the Readiness Index, there is little chance of any rider winning an Olympic gold in mountain biking unless they are world champion before 23. “I think that will make it 100 times more special if I do get a medal at the Olympics, because it’s just like one in a million,” says Richards. “We haven’t got one for so long.”

Those at British Cycling have every incentive to play up the idea that it is a futuristic sports laboratory in which brains and moxie combine to conquer the world. If marginal gains was the explanation for past golds, the Readiness Index is a ready-made answer for the next haul.

Some, though, wonder if there are more shadowy reasons behind the triumphs. Michaël D’Almeida, a French sprinter, echoed these doubts when he spoke to reporters in Rio. “We are human beings like them, we are made of the same stuff, we have a bike like they do, so why are they better? If I had the explanation, I wouldn’t be here today with a bronze medal around my neck. I’m not in their camp, in their country. I don’t know how it works. I don’t know what goes on. I have my ideas about certain things.”

British Cycling’s programmes director Andy Harrison © Nadav Kander

Such insinuations have existed for years. While British Cycling does appear to be a regime willing to push every limit to win, a systematic doping culture seems unlikely. The UK’s anti-doping agency is considered to be one of the world’s best, and British Cycling headquarters is relatively accessible to the public. “This organisation has got a really strong anti-doping and compliance culture and attitude,” says Andy Harrison.

Recent events show why the doubts continue. In 2009, Brailsford formed Team Sky with the outlandish ambition of a British rider winning the Tour de France within five years. Unlike past victors, notably the disgraced seven-time champion Lance Armstrong, Brailsford said they would win it clean. British Cycling and Team Sky retain close connections, sharing the same headquarters and some overlapping staff. Many Olympic riders graduated to the professional road team including Sir Bradley Wiggins who, in 2012, won the Tour. He wore the race victor’s yellow jersey while ringing the bell to signal the start of the London Games.

This September, following a cyber hack of the World Anti-Doping Agency (Wada), it was revealed that Wiggins had secured a Therapeutic Use Exemption (TUE) before the 2012 Tour. The exemption allows athletes to take banned substances for medical reasons with the approval of sporting authorities. Wiggins took triamcinolone, a powerful steroid, and said he did so to clear up symptoms related to asthma and pollen allergies. The TUE was known about by Brailsford and applied for by the team’s doctor, Richard Freeman, who now works for British Cycling. There is no suggestion any anti-doping rules were broken.

It’s not a cushy world. It’s sport

This autumn UK Anti-Doping also started an investigation into British Cycling and Team Sky after reports that a British Cycling coach delivered a medical package with unknown contents to Freeman during the 2011 Tour de France. (Wiggins, Team Sky and Freeman declined to comment, with the doctor citing medical confidentiality.) Executives from both groups have been asked to appear in front of a parliamentary committee investigating doping in sport.

Such developments are damaging, says David Millar, a former British road cyclist. When Millar turned professional in 1997, he was told he stood little chance of winning while competing clean. By 2001, he was using the blood-boosting agent erythropoietin (EPO). He stopped in 2003, only to be arrested a year later when French police found two used syringes in his home. Millar wrote recently that the evidence was “tucked away on a bookshelf as a morbid reminder of what I’d done”.

After a two-year ban, Millar returned as a prominent anti-doping campaigner and, in February, British Cycling appointed him as a mentor to the academy riders. Millar believes the country’s cyclists are now brought up in a clean system. “I’ve got two sons, five and three,” he says. “But if they were 18 and 20, I’d be completely fine with them going into pro cycling now. Quite a few years back, I’d think, ‘No way are they going anywhere near that sport.’”

David Walsh, the Sunday Times journalist who exposed the doping of Lance Armstrong, says an asterisk must be placed against Wiggins’ victory. “The team that wanted to be seen as whiter than white had been dealing in shades of grey,” wrote Walsh in September. “What they did was legal, but it wasn’t right.” When I asked about Walsh’s verdict, Millar says: “I don’t know how I feel about that. I think the saddest irony is [British Team Sky rider] Chris Froome [was in] second place . . . It’s just a sad situation because it never should have really happened. But whatever happened, [Team Sky] won the Tour de France.”

© Nadav Kander

British Cycling’s determination to test every limit has led to other problems as well, notably in its uncompromising approach in training. In 2014, head coach Shane Sutton was promoted to technical director and tasked with leading the Olympic team to glory. The plan was knocked off course in March when Jess Varnish, a 25-year-old sprinter, was cut from the team. Soon after, she complained of a macho and bullying culture at British Cycling.

Varnish claimed Sutton had told her she was “too old” and to “go and have a baby”. Further accusations emerged from Paralympic riders complaining that Sutton called them “gimps” and “wobblies”. Sutton stepped down but denied the allegations. In October, British Cycling said that, following an internal investigation, its board upheld Varnish’s allegation that Sutton had used “inappropriate and discriminatory language” and expressed “sincere regret” over the incident. A separate review by UK Sport is due soon. Sutton did not respond to requests for comment but has told The Telegraph that he maintains his innocence: “I have definitely never overstepped the mark with Varnish or any other athlete.”

Last month, another pillar of British Cycling departed when chief executive Ian Drake announced he was stepping down next April after seven years at the helm. People close to Drake say he had wanted to leave earlier but the furore over Sutton had delayed his plans. The organisation is now searching for candidates to fill its two most senior positions. Reports suggest Sara Symington, a former cyclist and head of England Netball, is frontrunner to become the new performance director.

In October, 150,000 people lined the streets of Manchester as Britain’s Olympic and Paralympic teams paraded through the city on open-top buses. Prime Minister Theresa May said the northern city was the appropriate place to hold celebrations because it had “been an important focal point for elite sport”, a nod to British Cycling’s place at the centre of the country’s sporting excellence.

Those revellers were among the millions of Brits glued night after night to track cycling from Rio this summer. For now at least, the public appears happy to bask in reflected glory rather than question the methods used to achieve such victories.

© Nadav Kander

“It’s not a cushy world,” says Clancy. “It’s sport . . . The day will come when those guys turn round to me and say, ‘Ed, we don’t think you’re capable of getting an Olympic medal in the next Olympics. See you later.’ And that’s just the way it is.”

If the Readiness Index goes according to plan, today’s academy riders will be on the next parade bus. “Decisions that were made over the past two years will determine whether we are successful in 2020,” says Harrison. “And decisions we make in the next two years, whether we make the right selections on a 15-year-old, will determine whether we step on the podium in 2024.”

Yet, the current tumult may have a lasting impact. “They need to fix it quickly,” says Millar about the organisation’s current crisis. “They need to get it all back on track, which I do believe they can do. The blueprint is there.” Meanwhile, the Olympic wheel is turning. British Cycling cannot afford to wobble now.

Murad Ahmed is the FT’s leisure correspondent

Photographs: Nadav Kander