1999–2002 :Title Hat-trick,Retirement Plan

Schmeichel's decision to leave United after eight seasons prompted Ferguson to bring in replacements: Mark Bosnich from Aston Villa and Italian Massimo Taibi. The latter featured in four matches, the last of which a 5–0 defeat at Chelsea in October 1999; he was not selected again by Ferguson. United ended the 1999–2000 league season as champions, with just three defeats and a record points margain of 18. In the mid-season, the club beat Palmeiras in Tokyo to win the Intercontinental Cup, but exited with apathy at the Club World Championship.United failed to retain the Champions League, out in the quarter-final stage to eventual winners Real Madrid. Ferguson sought to strengthen his squad and monitored the progress of Ruud van Nistelrooy, who he described as "a striker of the highest calibre". He met the player and his agent in Manchester to discuss formalities and was informed of Van Nistelrooy's knee injury. Ferguson recalled from past experience that he was not "terribly perturbed" and pushed ahead with the transfer. Van Nistelrooy however failed his medical, at which point Ferguson spoke with him, "emphasising that we might yet find a way out of the nightmare." The deal was resurrected a year later, for a British record transfer fee of £19 million. To solve the ongoing goalkeeping problem at United, French goalkeeper Fabien Barthez was signed from Monaco for £7.8million.
In the 2000–01 season, United retained the league title for a third season and became only the fourth side in history to do so. The achievement was overshadowed by reports of a rift between the board and Ferguson regarding his future at the club. Ferguson told MUTV in May 2001 that he was prepared to sever all ties with the club once his contract ended the following year: "The decision has been taken. I'm going to leave the club. I'm disappointed with what has happened because I was hoping something would be sorted out. It hasn't happened as I thought it would and that's all there is to it." However weeks after, both parties reached a compromise, which pleased Ferguson: "I am delighted we've settled this. When you have been at the club as long as I have it gets in your blood."
United were active in the transfer window once more and signed midfielder Juan Sebastián Verón from Lazio for a reported £28.1 million. Ferguson was interested in bringing both Patrick Vieira and Sol Campbell to the club, who both later committed to Arsenal. Before the 2001–02 season had begun, McClaren left to become Middlesbrough manager; Jimmy Ryan was named assistant to Ferguson for the duration of the campaign. In August 2001, United sold Stam to Lazio for £16 million. The transfer was said to have been instigated because of claims made in the player's autobiography Head to Head. Stam suggested that Ferguson illegally contacted about a move to Manchester United, before informing his club PSV. Ferguson commented that the club needed to recoup the big money spent in the summer; Stam therefore left to balance the "massive wage bill". Ferguson replaced the defender with Laurent Blanc, a long sought after target. In an interview with Alistair Campbell eight years after, Ferguson described his biggest mistake at the club was "letting go of Jaap Stam. No question." United endured a poor first half to the season, whereby they languished in ninth position after a home defeat to West Ham United in December 2001. In spite of putting together a run of eight successive wins during the winter period to move up in the table – this coincided with Ferguson's decision to remain at the club until 2005 – United finished third, behind champions Arsenal and Liverpool. United were also unsuccessful in Europe and lost their Champions League semi-final on away goals to Bayer Leverkusen, Early exits from the League Cup and FA Cup meant that the season ended trophyless. Ferguson himself admitted that the decision to pre-announce his retirement had resulted in a negative effect on the players and on his ability to impose discipline.