The 28-year-old frontman had broken his metatarsal against Chelsea in the lead up to the tournament in Germany, and the Manchester United boss was adamant he would be unable to feature for England.
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"Leif [Sward, England doctor] and I met Ferguson and United's doctor at the United training ground," the Swede recalls in his new autobiography.
"'He cannot play in the World Cup', Ferguson said flatly. The doctor brought out some X-rays that he said showed Rooney's broken bone would not heal in time.
"When the doctor finished, Leif looked him in the eye. 'Why do you sit here and lie to me?' Leif asked.
"He was one of Europe's foremost specialists on this kind of injury. I just wish I could have filmed Ferguson's face when Leif explained that Wayne's break would heal in time for the World Cup.
"When Leif had finished, I turned to Ferguson. 'Sorry, Alex,' I said. 'I will pick Rooney'.”
Rooney was eventually passed fit for the tournament but failed to score a goal in his four appearances before being sent off in a penalty shoot-out defeat against Portugal for stamping on Ricardo Carvalho.