In just a couple of days, a TV network which has been kicking goals on screen this year with a succession of winning prime time shows has ended up in the headlines looking like a vengeful, backtracking basket case.
Wilkinson's shock exit was compounded on Tuesday with news Nine had axed founding host Paul Vautin from the long-running NRL Footy Show.
Then Nine CEO Hugh Marks - himself the recent beneficiary of a pay rise which saw him take home $2.77 last financial year, despite Nine's $203 million annual loss - took the unprecedented step of outlining publicly why he thought Stefanovic was worth more than Wilkinson. Complete with dollar figures.
It further fuelled anger over Wilkinson's exit among her supporters, and mystified many in the industry.
THE LISA FALLOUT
"Nine has handled this with the same bunker mentality we saw over their reaction to 60 Minutes in Lebanon," TV commentator and TV Tonight editor David Knox said.
"Trying to paint Lisa Wilkinson as greedy is a bad look for corporate suits, when the audience already has affection for the talent. You can leak stuff to the press and let them do your work, but going on the record about contracts is a no-win."
Nine may have felt the need to put its side of the story across, but Knox was not alone in suggesting the wisest move might have been to acknowledge "It was checkmate. Cop it on the chin. Move on to the next game".
"Nine is in damage control because the narrative (around Lisa's exit) became one surrounding gender pay parity," Knox said.
"That drags us back to the awful days of Nine's boys club, which frankly is consigned to history. "But to divulge someone's salary and suggest ten producers would have to go is not only impolite, it actually feeds into the gender parity.
"When men score a mega-salary there are high fives all around. Karl stitched up a super deal with pal David Gyngell. Eddie did the same when he moved from CEO back to talent.
"Hugh Marks was recently rewarded with nearly $900,000 in bonuses. Why is it women are the ones who are supposedly so greedy?"
As fallout continued over Wilkinson's sensational defection to Channel Ten, Today yesterday enjoyed a spike in the ratings, as viewers tuned in to see the panel's reaction to life after Lisa.
Today on Tuesday morning averaged 301,000 viewers to rival Channel Seven Sunrise's 262,000.
The week before, Today's Tuesday figure was 237,000, with Sunrise winning that day's ratings.
On Monday, with Wilkinson still at the desk, Today had 274,000 viewers.
THE FOOTY SHOW
LESS than a week after announcing at their programming showcase that Paul Vautin, Erin Molan, Beau Ryan and Darryl Brohman would be returning for a 25th season, Nine axed The NRL Footy Showas viewers had known it, as well as Vautin.
In the process, it managed to overshadow the fact it had just solidly backed rising talent Molan, and a determination to win back female footy fans.
Molan, who was front and centre at last week's upfronts, was installed as host, but as the changes to the show emerged on Tuesday, even she was forced to admit she wasn't sure what the arrangements were.
"I'm not sure what the show will look like next year but I am so grateful for the past six seasons alongside Fatty, Big Marn, Beau and Glenn (Pallister - the show's executive producer, who has also moved on) and the whole team," Molan told The Daily Telegraph.
The fact Vautin was told while holidaying overseas he was gone, and would see out his career in the commentary box, Brohman's confession "none of us have been told what's happening" and the lack of clarity over Ryan role obscured the message.
The decision to rejig the show makes sense in financial and ratings terms. But the way it unfolded almost turned kicking a goal into an own goal.
"Backtracking on an upfronts statement is never a good look," Knox says.
"And this one was arguably record time.
"Sometimes it is better to put out the bad news a week earlier, such as a show being axed, so that your good news swamps it days later. Not the other way around."
Vautin, who over the years has expressed amazement and delight at his TV longevity post-football, seemed to remain in the mindset when spoke about getting the heave-ho as host.
"In the end, nothing lasts forever," he wrote to WSFM's Brendan Jones. "I had a great run, especially for a short, chubby, redhead who played for both Manly and Queensland. That's not a career, that's a miracle."
Nine has had a big year on the ratings front, with wins in prime time and key demographics each quarter.
Among it big have been Married At First Sight, which arrested the take-all-prisoners ratings rule of Seven's My Kitchen Rules at the start of the year. Nine then ushered in The Voice, with the injection of new mentors Kelly Rowlands and Boy George drawing fresh viewer interest.
Its masterstroke was the first season of smash hit ratings winner Australian Ninja Warrior which debuted as ratings gold, and stayed rock solid. And Nine is about to finish a bumper season of The Block. A Current Affair has also consistently won it's timeslot.
"Nine has had a very strong year," Knox says.
"At the upfronts there were so many renewals they were light on new titles. Ironically, that's a good position to be in. They have owned the second half of the year."
The fortunes fly in the face of this week's horror headlines.
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