Apparently new manager David Moyes convinced him to stay with the club and, at that point, it seemed the saga was over.
According to Paul Clennam of Goal.com, Nani is not pleased with his role on the team:
Goal understands the player feels he has been harshly treated by his new manager and, prior to his latest fitness setback, had grown concerned at a lack of playing time, particularly in a World Cup year.
A source told Goal: "The player is aggrieved at how the situation has developed. The new manager convinced him to sign a new deal which he agreed to, even though he was forced to settle for €48,000-a-week less than he was asking for.
"Nani could’ve accepted a far more lucrative offer from abroad in the summer but opted to knuckle down and fight for his place at Old Trafford. His attitude has been spot on in training and he feels aggrieved that he’s not been rewarded with first team opportunities."
United's response to this should be pretty simple—if Nani isn't happy at United and wants to leave, they should facilitate that move immediately, much like it appeared they would do this summer. It's not as though he's been a key figure for the team in recent memory.
Nani has made just 19 appearances in the Premier League in the past two seasons, scoring a goal and adding two assists in that time. He's earned a decent but hardly noteworthy 6.73 average match rating in the league this season according to WhoScored.com, a far cry from his 7.19 score in 2009-10, 7.58 in 2010-11 and 7.31 in 2011-12.
One problem for Nani's future at United is that Adnan Januzaj has been a revelation out on the wing this year, while Antonio Valencia and Ashley Young (once he returns from a shoulder injury) also require playing time.
Seeing as he's failed to distinguish himself when he's played this season, it's hard to imagine him carving out a significant enough role to cut back Valencia's or Januzaj's playing time.
Of course, selling him also won't be easy if United continue to value him at around €19 million, as Clennam notes the club is doing at this point, far more than they were dangling him for over the summer.
And with plenty of fixtures remaining on the season, perhaps the club simply feel they could use the depth.
But if Nani continues to disappoint out on the pitch and grumble off it, there is really no reason to keep him around. It might be a bit hasty to sell him during the January transfer window, but if the club receive the right offer, they shouldn't hesitate to cut ties.