The game was fewer than 15 minutes old and Wayne Rooney, in his new maroon substitutes' vest was down near the corner flag with Ashley Young, staring at the action with an intensity which looked like him disguising the fact that his omission from Manchester United's biggest match in a year and a half was searing through his head. Then the fourth official trotted up to tell him to keep off the pitch. You could only imagine the agony for a reserve who could not bring himself to put tracksuit trousers on like all the rest.

His manager had the explanation for the omission ready before the game began, reaching for the reason he has used several times this season that Rooney needs "a game or two" to be ready to play after injury. It's an aspect of the forward's football that he hasn't employed before this campaign and it's seemed less than complimentary, given that Ferguson cites Rooney's "frame" as the reason. As arguments in team selection went, it did not even stack up. Rooney has been back for two games since he missed a couple of matches with a sinus infection.

No, the absence went well beyond a manager's propaganda – even one as well versed in that art as Ferguson. In the match programme, where Rooney had agreed to an interview in anticipation of a lead role in another big United occasion, the striker said that "these are special nights and ones you want to enjoy. You just hope you can express yourself and hope the team wins." It was Roy Keane, in the ITV studio, who knew how much of a blow the starting XI was to him – a "massive" one. "He's a big player and he wants to play in the big games, and he'll be bitterly disappointed to be left out tonight," Keane said. "Wayne might be quite selfish about it and look at it and say the writing's on the wall for him."

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Ferguson has never lacked the bold spirit and willingness to wield an axe without flinching, when the big moments arrive. You can reach back to Jim Leighton and the 1990 FA Cup final replay for evidence of that, and the omission of Ruud van Nistelrooy for the League Cup Final 16 years later. And then the more poignant decision, in the context of tonight, to leave David Beckham on the bench against Real Madrid in 2003. He came on and proved, of course with his two goals, that he was worthy of better treatment than that. Beckham's contribution no more altered the course of United's quarter-final elimination than it did the course of his United career. He started the remaining three league games of the season and was gone that summer, away to Madrid. The same went for Leighton and Van Nistelrooy, each out within six months of their major omissions.

The noises Rooney has been making in the last few weeks have all been the right ones. "The age I'm at now is the time when most players start to peak – from now and across the next four or five years," he said earlier this week, in the course of discussing a landmark 200th goal for United – the target is only five away. Ferguson and he have moved well beyond the events of October 2010, when United's failure to sign "world-class" players were his stated reason for not signing a new contract before £250,000-a-week solved the problem.

But back then, he was the heartbeat of the club. Now Robin van Persie has that talismanic role. Ferguson signalled that he is not good enough for United on the biggest night of all.

Rooney, considered by Ferguson to be less of a threat than Danny Welbeck – a striker with two goals to his name all season – was left with fewer than 20 minutes to turn something up and that he had as little impact as across the course of the first leg in Madrid leaves him still searching for a match-winning display on the biggest stage. One to match George Best against Benfica in 1966 or Roy Keane's at Juventus.

His contract enters its final two years this summer. There can surely not be five more years of £250,000-a-week for a player not to start on the biggest stage. The fear that Manchester City would lavish £40m on Rooney was such a fear here back in 2010 that fans in balaclavas beat a path to his door – one wielding a banner stating "sign for City and you're dead". That City are no longer that kind of threat has nothing to do with them having less to spend. He is just no longer a £40m player. The Nani controversy can obscure it for only so long. The writing is on the wall.

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