United manager Sir Alex Ferguson overlooked Rooney in favour of Robin van Persie and Danny Welbeck and, despite suffering a 2-1 defeat by the Spanish side that sent United out of the Champions League, the decision was tactically vindicated.
Rooney's omission led to widespread media speculation that his days at Old Trafford were numbered but former England manager and United assistant boss Steve McClaren does not think he will leave the Premier League leaders.
"I know Wayne Rooney and all he wants to do is play football and win, all he wants to do is win trophies. He is a winner and there is no better club to be at than Manchester United if you are a winner. He won't want to leave unless told he can leave," McClaren told Sky Sports.
"Sir Alex will have spoken to Wayne about the reasons why he was left out against Real Madrid.
"It was a decision made in the best interests of United winning the game. United have so many big games and Wayne will be involved. At the moment I cannot see his future beyond Manchester United.
"There's only one way to go when you leave United and that's down."
Former United striker Michael Owen said leaving Rooney out against Real would have been a "real kick in the teeth" for the front-man, but given his patchy recent form and the glut of attacking options at his disposal, it is by no means certain that Ferguson will start him against Chelsea at Old Trafford.
Van Persie has established himself as United's top striker, scoring 22 goals since arriving from Arsenal last year.
Ferguson is a big fan of Welbeck's pace and work rate, while the livewire Javier Hernandez, a regular scorer against Chelsea, provides another potent attacking threat.
Shinji Kagawa scored a hat-trick against Norwich City last week playing in the hole behind Van Persie, a position Rooney has occupied frequently this season.
The 27-year-old Rooney has been United's heartbeat and main inspiration for over eight years.
But his recent form has fallen below the high standards he has reached consistently since marking his United debut with a stunning hat-trick in a Champions League game against Fenerbahce in 2004.
Rooney has scored 166 goals for the club, helping them win the Champions League in 2008 and four Premier League titles.
Playing alongside Ruud van Nistelrooy, Carlos Tevez, Cristiano Ronaldo and Dimitar Berbatov, Rooney has regularly found the net with spectacular 25-yard strikes, bullet headers and neat close-range finishes.
Ferguson has regularly deployed Rooney in a wide midfield role and although he has done an efficient and selfless job for the team, his impact in the opposing penalty area has diminished.
Niggling injury problems have also interrupted his season and Ferguson has always maintained that the chunky forward needs regular games to retain his sharpness.
The suspicion remains that 10 years as a Premier League forward have taken their toll on Rooney's body and Ferguson has never been af
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