Fletcher made just 15 appearances for the Red Devils last season as he struggled with ulcerative colitis, and has now been ruled out for the rest of this campaign having undergone surgery to cure him of the rare bowel condition.
Despite having signed a new contract at Old Trafford in March 2011, this latest setback has raised fears over the Scotland international's long-term future in the game, but Sir Alex remains adamant his countryman can return to the holding midfield role that he occupied for most of his 13 appearances this term.
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"He had to change his game and he hasn't been the Darren Fletcher of three or four years ago in the games this season," the United boss told the club's official website.
"Instead, he was sitting in front of the back four and he did well. That could be his role in the future. When he comes back, and I hope he does, it will be in a different role."
Sir Alex reveals he was unsurprised by the news Fletcher would require an operation to cure the problem, but concedes his absence will be a blow for both the player and the club.
"It was something we thought would happen anyway," he added. "He tried his best to cope with the condition with the treatments he was using but, in the last couple of weeks, it's come back.
"This operation will hopefully solve the situation and we expect him to be back in July. It's a blow for the boy but given he's been dealing with the condition for a few years, it's just another step for him.
"He has fantastic character, he's a brilliant boy. He'll do his best, no doubt about that. He always does."