The Portuguese club were in turmoil last month after several of their major players decided to cancel their contracts and leave after they were attacked at the club's training ground by fans.
The fans were agrieved at the team's poor performances in the league, whcih saw them miss out on a Champions League spot, and decided to physically attack the players and as a result several were arrested.
Major figures at the club such as Rui Patricio, Bas Dost, Gelson Martins and William Carvalho all decided to leave the club as a result of the attacks, with Fernandes joining them.
However, the club's president Bruno de Carvalho, who was blamed for provoking the attacks, was removed by the club's members.
The midfielder, who made 56 appearances for the club in all competitions last season, decided to go back on his decision and sign a new five-year deal with the club now that de Carvalho had been removed from his post.
"It doesn't matter who is to blame, now it is over. Sporting is opening a new page and I believe it will be very good" Fernandes told a press conference.