The shock omission from the starting line-up for United's biggest game of the season in the second leg of their last 16 tie against Real Madrid was overshadowed by the controversy surrounding Nani's red card and Ronaldo's Old Trafford return.
Before the game, manager Sir Alex Ferguson said the England forward was on the bench because he had not had enough match action after injury but afterwards, with Ferguson too upset to talk, assistant Mike Phelan said the move had been tactical.
"In that dressing room, everyone was fit," Phelan told a news conference after United went out 3-2 on aggregate after a 2-1 defeat on the night. "But big decisions have to be made."
Take David Beckham who started on the bench for Real's 2003 trip to Old Trafford before leaving the club that summer or Ruud van Nistelrooy who was benched for the 2006 League Cup final and a series of other games before departing that year.
"Maybe the writing is on the wall for him," former United midfielder Roy Keane said in the ITV studio before the game.
Once branded a "genius" by Ferguson, who persuaded him to stay at the club when he wanted to quit in October 2010, Rooney has been given a message he is no longer the main man.
He had a good chance to score after coming on against Real but sent his effort over, while players who were picked ahead of him were some of United's best performers with Danny Welbeck and Ryan Giggs at the heart of their best attacking moves.
Real manager Jose Mourinho said Ferguson's judgment over his line-up should not even be being questioned.
"Sir Alex has won the right for every decision to be correct and never have a question mark against them," he told a news conference. "He is the best. He is the top.
"You are nobody, I am nobody [to question his decisions]. He did a great job."
United's next team-sheets will be scrutinised for further clues about Rooney, starting on Sunday when they host Chelsea for a place in the FA Cup semi-finals.
