On a day when the Dragons merchandise van crashed on the way to WIN Stadium, Flanagan's future was left hanging in the balance as his side's winless season extended to a sixth game.
With Flanagan pacing the touchline for 80 minutes, the Dragons showed some spirit to fight back from 16-0 down and even led by two at one stage.
But ultimately the Sea Eagles' class out wide shone through, with Reuben Garrick bagging a double and Tom Trbojevic scoring one try and setting up another.
"I don't want to hide in the coach's box," Flanagan said.
"I am here to fight and here to win. I'm on the sideline with the team fighting as hard as I can.
"I didn't want to hide in the coach's box and have cameras going up there. They can get as much as they want, they can get me for 80 minutes if they want."
Flanagan has been a man under pressure all week, with the next fortnight against South Sydney and the Sydney Roosters before a round-nine bye crucial.
The Dragons were clearly an improved side on last week's insipid 32-0 flogging at the hands of North Queensland.
But ultimately it was a series of old-fashioned coach-killers that extended the club's worst ever losing streak to 10 games, with their last victory back in August.
With Anthony Seibold sacked at Manly after three games, Flanagan was asked on Friday if the rope was shorter now for coaches.
"I am not quite sure if the rope is shorter or longer, but it's not an enjoyable one when you're on that rope," he said.
"I've never experienced this, losing four or five in a row. It is different especially for the start of the season, but all I can ask is if the players put in a real good effort.
"That means they're playing for me. Tonight I thought they did put in a real good effort."
While the effort was there, so too were the coach-killers.
Filling in at fullback, Tyrell Sloan was highly involved in attack but dropped a ball before Manly's first try, then failed to stop a 40-20 in the lead-up to their second.
The Dragons let Manly go 100 metres from the kick-off through their third to Garrick with winger Christian Tuipoltu injured, and at that point the Sea Eagles were beating the clock.
After the Dragons got back to 16-12 down, winger Setu Tu dropped a ball over the line on halftime under pressure from Trbojevic.
Tu did well to score after the break and later hold up Tolu Koula to help the Dragons to an 18-16 lead, but there was more pain for to come.
Down 22-18 after Kobe Hetherington crashed over for Manly, the Dragons had a golden chance to take the lead with a huge overlap to their left.
But instead of putting it through the hands, back-rower Luciano Leilua opted to kick and put far too much weight on the ball and sent it dead.
Trbojevic sent Lehi Hopoate over shortly after, and with that the game was over as a contest, with Kieran Foran now two-from-two as a coach.
Down on the canvas a fortnight ago when Seibold was sacked, Manly could now be 3-3 if they beat North Queensland next week.
"The season was slowly getting away from us," Foran said.
"You have to stay in the pack. We have a really good footy team and we should be winning more games than we're losing."
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