"They'll never be just another club," the St George Illawarra coach said on Saturday.
"To win the first premiership for the club (in 2016), to go through what we went through."
This century, 22 coaches have returned to take on a club where they were previously full-time boss.
Several of those have come up against a team they won a premiership at, with Michael Maguire the last to do so in 2019.
But none have had a break up like Flanagan, who was effectively rubbed out of the game after the Sharks' 2018 preliminary-final loss to Melbourne.
The coach had little closure on his time at Cronulla, de-registered by the NRL for breaking the terms of an earlier suspension.
Flanagan has spoken at length on how he spent the next year disillusioned with the game and hiding in the dark corners of Shark Park to try and watch his son Kyle play in the NRL.
Six years on, he will return on Sunday as an opposition head coach for the first time - and in a very different mindset.
Flanagan (left) led Cronulla to 2016 grand final success. (Craig Golding/AAP PHOTOS)
He threw a jibe the Sharks' way after the Dragons' pummelling last week from the Sydney Roosters, and immediately copped some banter back from Cronulla chairman Steve Mace.
"It's just me firing a few people up," Flanagan said.
"Everyone in rugby league, when they're going up against their old club, look forward to getting there, and mark it in the calendar.
"I had a great time at the Sharks. It was the highlight of my coaching career. I go back there with fond memories."
Flanagan is not alone in returning to Cronulla on Sunday: St George Illawarra's Jack Bird will bring up his 150th NRL game following a horror run of injuries after he won the 2016 premiership at the Sharks.
The Dragons coach says the long-time utility has found a home at centre, declaring Bird's days in the back row over.
"He's fought really hard," Flanagan said.
"He was young and fearless when he debuted but he's matured and is more aware of things now.
"He's probably the fittest he's ever been - it's great to be there for his first game and his 150th."
The Flanagan sideshow has at least taken some heat off the Dragons' players after their 60-18 loss to the Roosters..
Flanagan admitted his charges were "embarrassed and quiet" returning to training this week, after being picked apart by Sam Walker on Anzac Day.
Nicho Hynes has the potential to be just as dangerous against the Red V on Sunday, with Cronulla having won the last seven against the Dragons by an average margin of 17.
"What happened last week is something we can't have and we've got to learn from it," Flanagan said.
"We've had no excuses, we've had to review it and move on to the Sharks."
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