United's prize asset seemed to be on his way out of Old Trafford after stating a desire to leave and publicly questioning the club's ambition.
But after an extraordinary few days of headlines, the 25-year-old striker performed a U-turn and signed a new five-year contract.
The reasons for the twists and turns throughout the week remain a subject of speculation, but Ferguson now wants the matter forgotten.
"It's all over," he said. "He's signed a five-year contract and we're happy with that, we kick on. It is all left in the past.
"It is our job now to kick on. We have got really important issues now, and that is chasing Chelsea. That is our main aim now, catching them up."
United are five points behind Barclays Premier League leaders and champions Chelsea ahead of tomorrow's home clash against Tottenham.
Ferguson has had plenty of experience in dealing with difficult situations with players in almost 24 years at the Old Trafford helm.
The Scot, who has guided United to 11 Premier League titles, usually emerges from them with credit, but does not want to take praise for another apparent victory.
He said: "I think there have been plenty of issues over the years at Manchester United. I suppose you could say that was a big one last week but only in the sense because it was a top player.
"There are plenty of players that come to contract situations that you have to deal with. The difference is they are normally done really quietly and unnoticed by most people.
"But there is always an issue with a player's contract these days. Every club has got them.
"The future is exactly the same as it was a few weeks ago. No-one has left the club, it is the same. We have the same squad of players."
On the field, United started to put last week's problems behind them by winning 2-1 at Stoke.
Having been criticised for surrendering leads throughout the early part of the campaign, United fans may have feared dropping more points when Stoke equalised late on.
But victory was secured when in-form Javier Hernandez won the game with his second of the afternoon four minutes from time.
"The area that is giving us the most concern is throwing games away," Ferguson said. "Throwing the game away against Fulham, Everton, West Brom - six points given away.
"We've actually given them all at least a six-point start. We have to catch it up."
Hernandez has now scored five goals in six games after following up his Stoke double with another decisive late goal against Wolves in the Carling Cup in midweek.
And with Rooney and Michael Owen injured, the Mexican's spell in the spotlight is likely to continue.
Rooney is on holiday in Dubai resting after suffering an ankle injury in training amid the confusion over his future, while Owen pulled a hamstring in training prior to the Wolves clash.
Ferguson is pleased with the way the 22-year-old Mexico international has settled at Old Trafford following his summer move from Estudiantes, but is not surprised by his success.
"We had a feeling he would break through. Therefore, if it gives you a problem, it is the right kind of problem," Ferguson said.
"There is plenty of evidence that the boy has got something and so far so good. He is keeping his place in the team because he deserves to keep his place."
Rooney was initially ruled out for three weeks when sidelined last week, but Ferguson has conceded the injury could be worse than feared.
"I think it may be longer," he said.