Thomas had to wait when mechanicals took out Diego Rosa, Mikel Landa and Gianni Moscon. Moscon's wheel front collapsed and he crashed.
"Over? For sure, races like this or Paris-Nice are won in seconds," said last year's Paris-Nice winner Thomas. "So to lose 1-20 in that is certainly not good.
"We'll try to be aggressive and make up for this, but I think GC is out the window now."
Footage of Rosa’s and Landa's incidents have yet to emerge. However, dramatic images caught Moscon trying to control his bike as something went wrong under him. The cause is uncertain, but his tri-spoke wheel broke to pieces.
Sky was the worst of the teams with overall favourites and the worst of the WorldTour teams. Their time of 25-02 minutes over 22.7km put them just ahead of four professional continental teams.
Thomas and Landa lost 1-20 to Thibaut Pinot (FDJ) and Nairo Quintana (Movistar), and slightly less – but still significant time – to riders like Adam Yates (Orica-Scott) and Tom Dumoulin (Sunweb).
"It was Murphy's law: what could go wrong did go wrong. We started decent steady but on the way back, we were really starting to shift.
"Myself and [Michal] Kwiatkowski and [Vasil] Kiryienka were feeling good and riding constantly at 61km/h. Then we hit two holes and three wheels just collapsed basically. And that just ended it,” Thomas said.
"The first one, Moscon was wiped out and took out 'Kiri', took him out the back, he didn't crash. It happened again and there were only four of us left, so we had to wait. It felt like forever, we were just freewheeling for a couple K. It's certainly not ideally."
The team's time is taken on the fifth man over the line. Sky and the other 21 teams began with eight-man rosters.
"We were just rolling, me [Salvatore] Puccio, Kawasaki [Kwiatkowski], and someone else. We had to wait for the fifth guy to come. Yeah, we lost everything there."
"I'm not so sure, I think it did," Thomas said when asked if there was more than one wheel collapse.
"Moscon's did obviously. From what the boys have said, I think Rosa's did. I think both of them had mechanicals, hit another hole. Yeah. It's certainly not ideal."
The team is riding on Shimano-made Pro wheels in Tirreno-Adriatico. Some were all-black without labels.
Head of technical operations Carsten Jeppersen would not comment, only saying that there were issues with three wheels.
A Shimano representative met with Jeppersen after the stage and took away the damaged equipment in two wheel bags, one double one and one single one. He only said that many teams are racing on the same wheels, including BMC Racing with the winning time of 23-20.
"We are investigating what happened," Shimano press officer Ben Hillsdon told Cycling Weekly by telephone later. "I've seen the footage and wee need to look at what happened."
Thomas and Sky must re-focus now that the "GC is out the window." They have six more stages to race, including one 16.1km summit finish to Monte Terminillo.
"We'll race hard and just try to tackle each stage," Thomas said. "I think we have a guy who can win on most days.”
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