Things didn't improve much for the visitors.
They slumped to 39 for 6, then 75 for 9 inside 29 overs. That brought the big Southlander Jacob Duffy to the crease. With nothing to lose he plundered a fast 31 off 30 balls, with 5 fours and a six.
Matt Bacon hung around with him as the last wicket added 33, the biggest partnership of the innings, and Otago were all out for 108.
"Everyone bowled nicely this morning," said Boult between innings, "so it was a good start to the summer ahead."
He'd no doubt be thinking his work for the day was done after taking 3 for 23. Fellow Black Cap Neil Wagner also took three wickets. James Baker and Colin de Grandhomme took two each.
Otago were all out before a delayed lunch break. Amazingly a star-studded Northern Districts team were almost all out before tea.
Henry Cooper went in the 5th over, caught behind off Duffy, and the decent-sized crowd sat up as Kane Williamson came to the crease just before 2pm.
Surely, it was finally time for some class batting from one of cricket's finest. It wasn't to be. The Black Caps captain nudged a single before playing tentatively forward to the other opening bowler Nathan Smith, and the keeper took an easy catch off the edge.
And that was mostly the story of the afternoon session. Dean Brownlie, BJ Watling and Colin de Grandhomme, all current or former internationals, scored five runs between them.
Not that they're there to bat, Ish Sodhi and Neil Wagner don't add to that total.
Flynn stood firm for 80 balls before he tried to square cut a shortish ball from the off spinner Mark Craig but hit it straight to point. He'd made a fighting 27.
The other ray of batting hope for ND was Darryl Mitchell, who also worked hard on a demanding pitch.
Boult, probably not expecting to bat, joined him just before tea with his team tottering at 59 for 8 and decided like Duffy that he may as well invoke some of his famously inventive and highly unorthodox stroke play.
Sadly, after a bit of post-tea fun when Boult had crushed a couple of fours and a six, Mitchell tried to join in but only skied an easy catch to deep point. He'd be kicking himself after doing the hard work.
Cue some vintage Trent Boult. With nothing to lose, and with his batting coach long ago having abandoned orthodoxy, Boult slapped and banged his way to the team's top score.
He took a particular liking to Craig's off spinners. In the Otago captain's 4th over Boult smashed him on to the bank for 6 on three consecutive balls. He took a dot ball, then came back strongly with a four and a six to complete the over. He'd brought up his 50, then gone to his highest first-class score.
Craig may have conceded 28 off the over but he was courageous. He put himself back on again and Boult couldn't stop swinging. It was a good time but a short time. Rutherford took a great catch on the boundary and Boult was out for 60. He'd been the main reason Northern Districts had a first innings lead 28.
There were 22 overs remaining in the day's play as Otago began their second innings just before 5pm.
Brad Wilson completed an unhappy day when he was out for his second low score of the day, LBW to Wagner, but then came the best batting of the day.
Hamish Rutherford and Shawn Hicks weathered the threat of Boult and Wagner to settle into some attractive strokeplay.
Hicks was especially good with some exquisite drives straight and through the covers.
He was 47 not out at stumps, Rutheford was on 37 and Otago at 88 for 1 lead by 60 with 9 wickets in hand.
