The Briton survived a day in hell in Sunday's ninth stage as big rival and long-time friend Richie Porte crashed out, but he lost his lieutenant Geraint Thomas, who also exited the race after a fall.
Froome is now without his key support, he could not drop his main rivals in the last climb to the Mont du Chat, and was also distanced by last year's runner-up Romain Bardet in the treacherous final descent.
In addition, Froome had to deal with controversy. Fabio Aru attacked him just as he was requesting assistance because of a mechanical problem on the Mont du Chat. Later Froome appeared to lean onto the Italian, who then almost crashed into the spectators lined up along the route.
"I lost my balance a little bit and swerved to the right. Aru happened to be on my right and he had to swerve as well. Any suggestion that it was on purpose is just crazy," said Froome.
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Both Froome and Aru played down the incidents - the attack and the alleged retribution.
To add to the off-bike worries, Sky found itself in the centre of a row over their time-trial skin suits at the Grand Depart in Germany, while team principal Dave Brailsford has been snubbing the media since his opening news conference, though Froome and his teammates have been cooperative.
The Welshman, who was more than willing to discuss team tactics and all things cycling when Sky arrived in the peloton, now declines to chat with reporters most of the time.
For the first time in years, the yellow jersey will not be holding his traditional rest-day news conference.
Though Froome picked up a four-second time bonus by finishing third on Sunday, he has not yet hammered the opposition.
He leads Aru by 18 seconds and Bardet by 51 going into the second week with the GC battle set to resume in the Pyrenees and the Frenchman, a runner-up last year, promising "more battles will be fought". But Froome has so far fought off his rivals.
"You need somebody on par with him and I don't know if that's the case. It's a race that could be Chris Froome's race," three-time champion Greg LeMond told Reuters.
Aru beat Froome in the first summit finish last Wednesday but was at some point dropped in the ascent to the Mont du Chat. Bardet was eventually reined in during the run-in to Chambery after dropping the main overall contenders in the descent.
One of Froome's main challengers, Colombian Nairo Quintana, is now 2:13 off the pace after failing to sustain the pace in the climb up the Mont du Chat. Even a podium finish, let alone overall victory, seems unlikely for the Movistar rider.
With a 22-km time trial favouring the Briton on the penultimate day, the race is still Froome's to lose.
(Reporting by Julien Pretot; editing by Mark Heinrich)
