Rooney goes from zero to hero as United cruise
Rooney gifted Stoke a surprise early opener at Old Trafford, but he recovered to equalise and further goals from Danny Welbeck and Robin van Persie extended the lead before Rooney's second brought up his 200th goal in club football.
That was enough to see off Stoke and ensure Sir Alex Ferguson's side remain in second place, four points behind leaders Chelsea.
Stoke stunned the home side after just 11 minutes with a goal that suggested a first win at Old Trafford in 36 years might not be beyond the realms of possibility.
Paul Scholes was at fault in needlessly and clumsily conceding a free-kick, tripping Michael Kightly near the right-hand corner flag and presenting Charlie Adam with the opportunity to whip a free-kick into the six-yard area where Rooney headed the ball into his own goal.
Stoke nearly scored again when Adam spotted a gap between goalkeeper David de Gea and his near post and chanced his luck with a low shot which the Spaniard did well to paw off his line to safety.
The fixture must have provided Ferguson with some discomfort, even before kick-off, when veteran defender Rio Ferdinand was the only United player to refuse to wear a "Kick Racism Out of Football" t-shirt.
Stoke's Kenwyne Jones did likewise, a protest led by the player and media pundit Jason Roberts, who believes the campaign is not doing enough to handle the issue of racism in the English game.
But it was the actions of Ferdinand, showing support for brother Anton who was at the centre of the John Terry racism storm, which will generate the greater headlines, particularly as Ferguson was vocal in his criticism of Roberts' position in the build-up to the game.
Down to the early goal, Ferdinand and his fellow United defenders were having an uncomfortable afternoon, particularly in dealing with the height of Peter Crouch in the Stoke attack and they should have been further behind on 24 minutes.
Kightly cleverly stepped over Crouch's pass for Jon Walters whose low shot from 16 yards was well saved by de Gea.
But the hosts were level on 27 minutes, a move started by eventual goalscorer Rooney.
The England forward, on the edge of the Stoke penalty area, found van Persie out wide and the Dutchman's excellent cross was met, clinically, by Rooney whose powerful six-yard header gave Asmir Begovic no chance.
Once level, United's forwards finally found some rhythm and Welbeck's teasing 20 yard shot clipped the top of the Stoke crossbar.
A minute before the interval, Antonio Valencia drilled over a cross from the right which van Persie met, having slipped his marker, to steer the ball past Begovic from the corner of the six-yard area.
It took only 51 seconds of the second half for United to extend their lead in similarly clinical fashion as Rooney sent over a perfectly-weighted cross from the right which Welbeck met, stooping to guide an equally well-judged header beyond Begovic.
But, after 58 minutes, Stoke were back in contention. Kightly collected the ball from Adam on the halfway line and sprinted towards the United goal, slaloming between three defenders and enjoying a fortunate bounce off an attempted Ferdinand tackle, before scoring from eight yards via the post.
It took only six minutes for United to restore their advantage, however, with Rooney claiming his second goal of the afternoon following a right-wing corner from van Persie.
The ball ricocheted off two defenders and Welbeck before falling kindly for Rooney to convert from close range at the far post.
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