Flanagan on Wednesday had his coaching licence provisionally deregistered after the NRL Integrity Unit uncovered emails that showed the 53-year-old broke rules by repeatedly communicating with the club during his 2014 exile for his role in the infamous supplements scandal.

He can appeal, but, even if the latest ban doesn't end his NRL coaching career, Flanagan's name has been muddied, likely forever.

Many will be pleased to see the back of him and hope he never returns.

But those close to the affable and approachable Flanagan, especially his players and ex-charges, will be shattered for a fatherly figure who refused to abandon them during the club's most turbulent period four years ago.

"I'm going to look after them. I've got to protect those players," Flanagan said as the drawn-out ASADA investigation took its toll.

"Some of them are only young boys."

Flanagan could never have imagined his coaching career unfolding quite like it has.

A nuggety hooker in his playing days, his seven-year, 78-game premiership career with St George, Western Suburbs and Parramatta was cut short by a knee injury in 1995.

But after being shown the coaching ropes by the great Bob O'Reilly at the Eels, Flanagan steered the Sydney Roosters to an undefeated Jersey Flegg premiership in 2004 before continuing his apprenticeship as an assistant to Ricky Stuart for two seasons at the Tricolours, then enjoying a four-year NSW State of Origin stint under Craig Bellamy.

He rejoined forces with Stuart at Cronulla before earning his big break at the Sharks when Stuart quit with six rounds remaining in 2010.

Flanagan guided the Sharks to the finals in his second full season in charge and immediately went to work on recruiting a series of NRL hard-heads including Luke Lewis, Andrew Fifita and Chris Heighington, in a bid to transform the club into a genuine title force.

Instead, his premiership plans - and world - came crashing down for a first time when banned for the entire 2014 season for his role in the Sharks' peptides saga.

The father of three always denied any knowledge of wrong-doing in the program but his decision in 2011 to introduce sports scientist Stephen Dank to the club had come back to haunt him.

A plumber by trade who once selflessly tiled the Sharks' gym, Flanagan feared he'd have to return to the tools.

Instead, he rebounded from his suspension to take Cronulla from the wooden spoon to the semi-finals in 2015.

But that was merely the appetiser to the main course as Flanagan's men - led by Clive Churchill Medallist Lewis and try-scoring match-winner Fifita - finally ended the club's 50-year wait with a heart-stopping 16-12 victory over minor premiers Melbourne in the 2016 grand final.

The emotional breakthrough reduced skipper Paul Gallen and club legend Andrew Ettingshausen to tears in the immediate aftermath.

But there will be tears of a very different kind now for Flanagan and his fiercely loyal Sharks clubmates after the latest devastating twist in the popular coach's rollercoaster career.

Australian Associated Press