The Scotland captain has been trying to manage a career-threatening bowel condition.
And after a brief Champions League appearance against Galatasaray last week, Fletcher took a major step forward at Old Trafford by leading the Red Devils to a 2-1 Capital One Cup victory over Newcastle.
"It is great to be back," midfielder Fletcher said.
"I have had a few reserve games and a run-out in the Champions League last week but it is good to be back, especially at Old Trafford, and in a winning team as well."
Goals from Anderson and Tom Cleverley were enough to book a last-16 meeting with fellow Premier League heavyweights Chelsea at Stamford Bridge next month.
In a seven-day period beginning on October 28, United will meet Chelsea twice in addition to taking on Arsenal at Old Trafford.
It represents a major test, not least because of their growing number of injured defenders, and Nemanja Vidic and Phil Jones will both still be sidelined for certain.
The departure of Alex Buttner before the end was another worry for Ferguson.
However, there was consolation in the performances of youngsters Scott Wootton and Michael Keane, who until the final 20 minutes when Papiss Cisse scored kept Newcastle at bay in impressive fashion.
"For two young centre-halves playing against top strikers they were fantastic," said Fletcher.
"They were talking to me the whole game."
Keane went into the match with just one substitute appearance under his belt, while Wootton was making his debut.
Marnick Vermijl, Robbie Brady and Ryan Tunnicliffe, whose dad landed a hefty wager at 100-1 that his son would play a first-team game for United - struck when the midfielder was only nine - were also given their first experience of senior combat.
Newcastle boss Alan Pardew was disappointed with the outcome, although he did sense a change in Cisse, who was scoring for the first time this season and hit the bar late on with a spectacular attempt.
"That goal means everything to him," said Ferguson.
"There is nothing in his workrate that has changed. Sometimes a goal can make a difference.
"You could see that little bit of exuberance return to his game with the overhead kick. I thought that was in."