Rooney reaches crossroads in Man United career
There was widespread incredulity at Old Trafford on Tuesday when the publication of the team-sheets for the last 16 second-leg match revealed that Rooney would be starting the encounter in the dug-out.
Rooney's disappointment will only have been compounded by the sight of his junior colleague Danny Welbeck taking up his usual role as the withdrawn striker in a 4-2-3-1 formation.
Robin van Persie's arrival from Arsenal last year had already obliged Rooney to play second fiddle in the United attack, but until Madrid came to town, the former Everton man had appeared to be manager Alex Ferguson's preferred partner for him.
Rooney eventually entered the fray as a 73rd-minute replacement for Tom Cleverley, but he was unable to turn the tie in United's favour, with his best chance a close-range volley that whistled over the bar.
United's assistant manager, Mike Phelan, insisted the decision was "tactical".
"Big decisions have to be made," he said. "The manager made those calls and we had the balance just right."
In the aftermath of the game, much of the attention in the British media has focused on Rooney's future.
The Times reported on Thursday that "Manchester United are willing to sell Wayne Rooney in the summer", while the Daily Mail claimed the striker was facing "a desperate fight" to save his Old Trafford career.
The speculation marks a complete turnaround from the events of October 2010, when Rooney accused the club of lacking ambition and was only persuaded to stay by a lucrative new five-year contract.
Since signing from Everton as a prodigiously gifted teenager in 2004, Rooney has enjoyed a glorious United career, winning four Premier League titles, two League Cups and the 2008 Champions League.
Though only 27, his 195 goals for the club put him in fourth place in United's all-time scoring chart, trailing only Bobby Charlton, Denis Law and Jack Rowley.
It had been assumed that Rooney would see out his playing career at Old Trafford, but although he remains a focal point for the English national team, Ferguson is reported to harbour concerns about his fitness and attitude.
The Scot has shown a ruthless lack of sentiment in the past, with Roy Keane, David Beckham, Ruud van Nistelrooy and Jaap Stam among the former United stars able to tesify to the speed at which his opinion of a player can change.
However, as former United team-mate Michael Owen has acknowledged, if Rooney does elect to leave, there are not many clubs with a big enough budget and profile to attract a player of his status.
"Sometimes when you're at the level he is at, you don't have many options," Owen told British radio station talkSPORT.
"If you are a mediocre player, you have 20 teams in England and aboard that you can move to.
"If Wayne Rooney moves, where does he go to? Real Madrid, Barcelona, Bayern Munich, Manchester City, Chelsea and PSG -- there's only half a dozen teams."
Owen says Ferguson's decision to drop Rooney for the Madrid game was "a real kick in the teeth", but with United vying for silverware in both the league and the FA Cup, he could still play a decisive role this season.
United host Chelsea in the FA Cup quarter-finals on Sunday and Ferguson's team selection could provide an indication as to whether Rooney's fall from grace at Old Trafford is temporary or terminal.