The only question was whether the Welshman would take the 1min 13sec required to snatch the maillot jaune off Alaphilippe’s shoulders. Or whether he would simply take a sizeable chunk out of his deficit, delaying the inevitable for a day or two longer.
Instead, in a result which has electrified this race and set up a tantalising tussle on the Tourmalet on Saturday, Alaphilippe went out and beat everyone, becoming in the process the first Frenchman to win a Tour time trial since Christophe Moreau in 2001 and the first French rider in the last three decades to win a Tour stage wearing the yellow jersey.
It was an extraordinary day, capped by Thomas declaring his rival to be the new race “favourite”.
Thomas had not done all that badly himself. Going out second last, the Ineos team leader blazed his way around the rolling 27.2km route, setting a time 22secs quicker than Lotto-Soudal’s Thomas de Gendt.
Alaphilippe, though, was in inspired form. Perhaps it was the crowds, who roared their hero around the course on the 100th anniversary of the maillot jaune. Perhaps it was the yellow jersey itself, which is said to give its wearer wings.
Inevitably there were those who suggested something more sinister. “I am not thinking about that at all,” Alaphilippe said dismissively of those who might suspect his performance. “I never imagined that I would win a time trial with the yellow jersey and start the mountains with the yellow jersey. I am not here to answer to suspicions.
“I know the work I have done to be here. I am the most surprised at where I am now. If it creates suspicion, I know being first always makes people talk. If I was last on GC, I wouldn’t have this kind of question. I ride my bike the way I like, everything else makes me laugh."
Whatever it was, the Frenchman was always up on the required pace. His advantage over Thomas stood at six seconds at the first two intermediate checks, dropped to five seconds at the third, before increasing to a massive 14 seconds by the finish, thanks largely to the manner in which the 27 year-old shinned up the final 17 per cent ramp.
The “favourite” tag Thomas bestowed on him is probably still fanciful. It is unlikely even Thomas - who complained of suffering a little in the 30C heat - really thinks that. The race hits the high mountains on Saturday, with a summit finish on the fabled Tourmalet, the first hors categorie climb of this race and the first over 2000m. And Ineos are likely to ride at a fierce tempo to try to put Alaphilippe in trouble.
It is going to be high drama at high altitude. Alaphilippe won the mountains classification last year, and can climb like a goat. But he is more of a punchy classics-style climber, preferring shorter, steeper ramps to 19km slogs at 7.4 per cent. If the Frenchman makes it up on Saturday without any fuss, though, there really will be some nervous punters on the Ineos bus.
Alaphilippe himself was quick to play down his chances of staying in yellow for much longer. “I don’t think so,” he replied, when asked whether he could hold on to it until Paris. “I just want to continue day after day. I hope to continue to surprise myself.”
On va voir. It was actually a double whammy for Ineos, with Egan Bernal having a tough day on the bike, losing 1min 44sec to Alaphilippe and dropping to fifth overall at 2min 52sec. And a double success for Deceuninck-QuickStep with nominal GC leader Enric Mas going above Bernal into fourth place at 2min 44sec and taking the white jersey for best young rider off the Colombian in the process.
Others saw their hopes completely blown away on the hills around Pau. Wout van Aert [Jumbo-Visma], the Belgian cyclocross star who won Monday’s sprint into Albi and has generally been one of the big success stories at this race, hit a metal barrier at 40kmh and had to be taken to hospital with a nasty gash to his leg.
Of the GC contenders, Nairo Quintana [Movistar], Adam Yates [Mitchelton-Scott] and Dan Martin [UAE] all shipped around two minutes to Alaphilippe, slipping down the rankings.
“[Alaphilippe] is obviously going really well,” Thomas conceded. “He’s certainly the favourite and the one to watch at the minute. [But] there’s a long way to go and a lot of hard stages to come.” Starting today. The Tourmalet awaits, with Ineos, unusually, on the back foot for once.