The Sharks have had five players involved in the 2017 State of Origin Series and although James Maloney missed Saturday night's loss, the other four players backed up in various emotional states.
Valentine Holmes was riding the high of Queensland's win but rotated with Gerard Beale between wing and fullback, Andrew Fifita's Origin heartbreak was offset by the birth of his third child and Jack Bird and Wade Graham carried the burden of the Blues' defeat into the clash with the Titans.
But rather than blame any Origin hangover for the loss Flanagan insists it is on the training paddock where Origin has had its greatest impact on the Sharks, demanding his players now put that to the side and finish the regular season strongly.
After dropping their Round 16 game to the Sea Eagles the Sharks appeared to have turned a corner with a 44-12 dismantling of the Roosters a week later but Flanagan said that only served to prove how good they can be with the right preparation.
"What I was pleased about for the Roosters was I had my top squad to train for a week," Flanagan said post game.
"All sides are doing it and who handles it the best gets through the Origin period but there's three Origin camps, 10 days of camp, we're missing five players for 30 days of the past six weeks.
"It's not great for a footy team to train like that and we're over that now so there's no more excuses.
"We've just got to put our head down, work really hard and get some results on the way home.
"We can set sail for home now but we've got a lot of work to do. Nothing's a given in this competition.
"We're not in the top four. We've done okay but we need to re-focus now, which we will."
Not part of a New South Wales Origin campaign for the first time since 2016, Sharks skipper Paul Gallen was a little more forgiving for how his side had managed the Origin period.
Prior to Saturday night Cronulla had won three of their five games since the Origin players went into camp for Game One but Gallen acknowledged the disruption that comes with having such a strong representation across both teams.
"To have five in it is huge and to train without your five best players for 30 days out of the past six weeks is very distracting," said Gallen.
"Thankfully it's over. I think we've handled it okay but we've got no excuses anymore from next week. We've got to start stepping it up.
"We've probably won more than 50 per cent of our games throughout the last six weeks so I think we've handled it okay for our biggest representation probably ever."
Gallen admitted that after such a comprehensive win against the Roosters that he was somewhat mystified as to why they fell so short against the Titans, refusing to blame the atrocious conditions for their display.
"The Titans just wanted it a bit more than us tonight," he said.
"We weren't good. They always seem to lift against us. It's a pretty disappointing result for us considering how well we played last week and how well we completed.
"To complete the way we did tonight and leak that amount of points, it's not real good."