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You're right; having actually read it fully, the headline is (predictably, I suppose) quite misleading.
Towards the end it says:
"Brailsford said: "We had two leaders - Chris was the actual leader,
Geraint the protected second leader - and the moment it dawned on him
that he wasn't going to win, Chris immediately switched to supporting
Geraint."
Harry -
Thomas was the perfect candidate to be the protected rider with the Froome case hanging over the team. If Froome was prevented from starting the Tour, then Thomas would have happily led Sky. With Froome starting, Thomas' lack of ego meant he was happy to accept the second leader role and, probably, happy to ride for Froome if required.
I think what few expected was that Thomas was the strongest rider in the race.
andyp
Well yeah, Sky clearly prepared Thomas to win the Tour in case Froome didn’t start. Not sure what to make of that.