The England captain, deployed in a central midfield role this season, has been a peripheral figure in a team struggling to gel and his lacklustre performance in the 3-1 defeat at Watford on Sunday led to widespread calls for him to be dropped.
Rooney mustered one shot, did not play a single through ball and created only two chances for team mates with the nine corners and free kicks he took.
His defensive contribution was also negligible, failing to make a single tackle and registering one block and one interception in a tetchy 90 minutes during which his main priority appeared to be engaging in a constant dialogue with referee Michael Oliver.
"Alex Ferguson knew it more than three years ago...Wayne Rooney is no longer worth a place in the Manchester United team," veteran United watcher Jim White wrote in the Daily Telegraph.
"Slow of thought and legs, United are a side currently functioning as if running through custard and much of the blame lies with the continued selection, in the most critical position in the team, of a man who is playing on his reputation."
Mourinho has never been afraid to make tough decisions during his trophy-laden managerial career and he faces a huge one on the 30-year-old Rooney, who is four goals short of overtaking Bobby Charlton as the club's all-time leading scorer.
Rooney has been a key part of United's attack since scoring a brilliant hat-trick against Fenerbahce on his debut for the Old Trafford club 12 years ago after arriving from Everton.
In recent years, with his pace diminished, he has operated in an ever-deeper role.
Former manager Louis van Gaal played him in midfield towards the end of last season and he fill that role with negligible impact for England in this year's dismal Euro 2016 campaign.
Mourinho has opted to do the same, banking on Rooney's range of passing and experience to create chances for strikers Zlatan Ibrahimovic and Marcus Rashford.
But his lack of mobility makes United predictable and easy to defend against and Mourinho must be tempted to play the sharper Ander Herrera or a natural holding midfielder such as Morgan Schneiderlin to allow Paul Pogba more freedom to get forward.
United fans have voiced their concerns about Rooney on social media and radio call shows in a rising groundswell of discontent and Mourinho faces a tense few days in which to ponder the situation.
Although Rooney was unlikely to be in the squad to face third-tier Northampton Town in the League Cup on Wednesday, his selection for the Premier League game against champions Leicester City on Saturday has become the manager's burning issue.
(Editing by Mitch Phillips)
