In the Champions League semi-final second leg against Arsenal on 5 May 2009, Fletcher was sent off, ruling him out of the Champions League Final. Manchester United appealed to UEFA to have the red card overturned on compassionate grounds on 7 May 2009, but this was rejected on 11 May. Then-Inter Milan coach José Mourinho commented on his absence: "Fletcher is more important than people think ... he 'eats' opponents in defensive transition. I believe Xavi and Andrés Iniesta are happy Fletch is not playing."
The 2009–10 season saw Fletcher consolidate his place in the heart of the United midfield, starting all of United's important games. He opened his scoring account for the season with a double in the first Manchester derby of the season, a memorable 4–3 victory for United, twice putting United ahead before Michael Owen scored in the sixth minute of added time. He won the Man of the Match award for his performance. On 21 November 2009, Fletcher scored his third of the season, hitting a half volley from the edge of the area into the top corner giving United a 1–0 lead against Everton in a 3–0 win. This season also saw Fletcher and fellow midfielders Michael Carrick and Park Ji-sung deputise in defence due to an injury crisis that left Patrice Evra being the only fit regular in defence. They still managed to keep a clean sheet against West Ham United and concede only one goal against Bundesliga champions Wolfsburg in the Champions League. Fletcher was sent off during the match against Birmingham City on 9 January 2010 after two bookable offences. On 10 March, he scored the fourth goal in a 4–0 win in the second leg of United's last 16 Champions League tie with AC Milan, making the score 7–2 on aggregate. Following this, Fletcher captained United for the first time in the league match against West Ham and was later confirmed as United's vice-captain, a position he held until December 2014. In April, Fletcher capped a successful season with selection in the PFA Premier League Team of the Year. On 9 May, the last day of the season, Fletcher scored the first goal of a 4–0 win at home to Stoke City.
Fletcher was Scotland's vice-captain under Alex McLeish, deputising in the absence of regular captain Barry Ferguson. Fletcher was named as full-time captain in November 2009 when Ferguson was banned from international football for misbehaviour.
Fletcher usually played as central midfielder in a box-to-box role, where he stood out for his physicality, tenacity, intelligence, and work-rate, as well as his energy and defensive ability, namely his tackling and marking. He was capable of playing anywhere in midfield, however, and also played as a right winger, in a holding role, and on occasion in defence; at international level, he also played in a more attacking role, due to his ability to get forward, which earned him comparisons with Steven Gerrard. In 2009, Terry Butcher described Fletcher as a "complete midfielder, a rare all-rounder and although he's a slightly different player to Roy Keane, he can become as great." He likened Fletcher to Bobby Charlton, noting that he "can get games by the scruff of the neck and inject pace and tempo," also adding that "[h]e understands the game, reads it well, is improving all the time and United rely heavily on him." While Fletcher was initially criticised in the media for his poor positional sense, a lack of creativity in his game, and his tendency to give possession away carelessly early on in his career, he underwent a technical and tactical development, which enabled him establish himself successfully in a deeper midfield role, from which he could dictate the tempo of his team's play in midfield with his passing; his playing style in this position was influenced by one of his idols, Fernando Redondo.
Fletcher was one of many footballers in the Manchester and Liverpool area whose homes were burgled while playing away games; burglars raided his house in February 2009 and held Grice at knifepoint. The incident occurred while Fletcher was in Milan for Manchester United's Champions League fixture against Inter Milan.