Not only are senior players under scrutiny, but other staff at Old Trafford are operating under a cloud of suspicion.
Key players - including Nemanja Vidic, Michael Carrick, Ben Foster and Nani - are all playing for their futures.
Off the field, chief operating officer Michael Bolingbroke has been side-tracked, interviewing employees about events following a staff party at the club's Red Café last month.
Feelings are running high among the 700 people employed at the club, but that won't get in Sir Alex Ferguson's way as he plans for the future of his squad.
The United manager is laying the groundwork for Serbian defender Vidic to leave next summer by routinely monitoring the form of Palermo defender Simon Kjaer.
The Danish centre-half has a release clause in his contract with the Italians worth £10million and is being primed for a move to Old Trafford.
Ferguson is also convinced Northern Ireland international Jonny Evans, despite acknowledging his lack of pace, will emerge as a top-class central defender alongside Rio Ferdinand.
The United boss is concerned because the volatile Vidic is becoming increasingly irritable, taking out his frustrations in training-ground tackles on junior players.
Federico Macheda and Danny Welbeck have been on the end of some crude challenges recently, part of an ongoing problem with Vidic identified in training.
Vidic's form has also dipped. He was sent off against Liverpool for the third successive game last month and returned to the team yesterday only because of injuries.
Other players are also in the firing line, with Ferguson contemplating the futures of Carrick, Foster and motormouth Nani.
Goalkeeper Foster's relationship with Ferguson reached breaking point following the 2-2 draw with Sunderland on October 3.
The United chief launched into his full hairdryer treatment in the dressing room after Foster's weak jump and mistake led to Kenwyne Jones' second-half strike.
Foster was immediately axed from the first team, replaced in goal by Edwin van der Sar against Bolton and losing his status as No 2 to Tomas Kuszczak.
It prompted a Foster outburst against Ferguson in the media, following his appearance for England in the 1-0 loss to Brazil, and although he has apologised for the controversial comments, Fergie is still furious with the keeper.
In his interview, Foster begged to be allowed to go out on loan to play first-team football and preserve his World Cup dream, but Ferguson slammed that door shut during talks last week.
The United manager has made it clear that he will not tolerate any more indiscreet comments from the keeper.
He has been told he is staying at Old Trafford, and ordered to battle it out with Kuszczak for the right to be van der Sar's understudy.
Under-performing midfielder Nani, who was expected to emerge from the shadow of departing Cristiano Ronaldo this season, but has been a huge disappointment, is another player in the firing line.
While away on World Cup qualifying duty last week, the Portugal international winger accused Ferguson of shattering his confidence.
Like Foster, Nani apologised for his incendiary comments during a meeting with the manager, but despite Ferguson's public backing, the tricky winger is clearly in the danger-zone.
Former West Ham and Tottenham midfielder Carrick is also uncertain of his position, with old club Spurs retaining an interest in a deal involving Croatia star Luka Modric heading for Old Trafford.
Ferguson believes England international Carrick, who has scored just once for United this season, should have more say in the centre of midfield.
Carrick's role is just one of several vulnerable positions Ferguson has pinpointed in the team, instructing his brother Martin to find replacements.
Despite long-standing interest in Valencia playmaker David Silva, there is a belief that he does not have the speed for the Premier League.
Other positions being considered are at left back, where Ferguson wants an understudy to the excellent Patrice Evra.
Despite showing promise after their move from Brazil, twins Rafael and Fabio da Silva have failed to make the grade.
Ferguson also wants another central midfielder next summer and a striker to support Wayne Rooney.
The United chief insists he will not spend big in the January transfer window, claiming his targets are all being quoted "around the £50million mark".
Ferguson said: "I am in the same position as I was in the summer. I don't see any value in the market.
"We get a million names thrown at us, all valued at £50million."
Instead, he will wait until the end of the season before he twists the Glazers' arms and demands sufficient spending power.
That will be tough, with post-World Cup transfer fees notoriously high, but Ferguson has promised his coaching staff he intends to rebuild the team again.
There is also considerable uncertainty off the field, with redundancies and cutbacks at United's Carrington training complex upsetting some staff.
In addition, the club's chief operating officer turned his attention to more pressing matters this week.
Bolingbroke and the club's human resources department have been in overdrive, interviewing staff about the events of Friday, October 23.
The club is awash with rumours after a staff party at the Red Café ended when some of them moved on to the Fantasy Bar in Manchester.
Staff earning between £18,000-£20,000 are living in fear of the investigation which centres on one high-ranking member of staff at Old Trafford.
Officially the club insist that "what staff did after the party at Red Café is of no concern to the club".