Ferguson looked on Tuesday like he was beginning to take it personally that a third top striker seemed to be heading out of Old Trafford in less than two years.
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After failing to replace Carlos Tevez and Cristiano Ronaldo with forwards of the same stature it will be time for a rethink if Rooney, whose 34 goals in all competitions enabled United to challenge for the title last season, walks out the door.
The manager has made it clear that door is still open for Rooney to stay, but after such a public declaration of shock that the striker wanted to leave, it seems Ferguson realises he will soon have to manage without him.
"I was dumbfounded, I couldn't understand it at all because only months before he'd said he was at the biggest club in the world and he wanted to stay for life," Ferguson told MUTV.
"We just don't know what's changed the boy's mind."
Ferguson has spoken previously of not wanting to get involved in the "kamikaze" spending of some of his rivals but it could be soccer suicide if he does not buy some established players in the next transfer window.
The world record fee of 80 million pounds received from Real Madrid for Ronaldo in 2009 has not all been reinvested, so the money for a class forward should be there despite United's 522 million pounds gross debt.
UNPOPULAR OWNERS
Fans are unhappy the club's American owners, the Glazers, have failed to provide more money for transfers and if there is no movement in the mid-season window, calls will grow for them to go the same way as Liverpool's former owners last week.
"They have saddled us with a huge debt and they are taking more and more money out of the club every season and the lack of net investment in the squad since they arrived is clear to all," the Manchester United Supporters Trust said in a statement.
"They've bought players but are they like-for-like replacements in terms of the quality of Ruud van Nistelrooy, Roy Keane and Cristiano Ronaldo?
"Our club is generating record revenues yet it appears we are unable to compete even with small clubs like Manchester City let alone Chelsea, Madrid and Barcelona."
With midfielders Paul Scholes and Ryan Giggs, defender Gary Neville and keeper Edwin van der Sar at the tail end of their careers, it is not just a Rooney replacement that fans will want Ferguson to buy.
His job will not be helped by a shaky start to the season - characterised by conceding late goals when leading to end up drawing matches - because for all his assertions they are "the best club in the world", United stand fourth in the league.
They need only look to Liverpool in the relegation zone for evidence of how quickly things can slide for big clubs.
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