Scown on stroke and Behrent appeared caught by this, being right back with Spain at the 500m mark as Great Britain swept ahead in 1m 46.43s, with the United States and Denmark boats chasing hard and South Africa just behind.
At 1000m, it wasn't even looking close with Glover and Stanning were now over 3.5s clear in 3m 36.72s.
However, in the battle for the minor placings the situation was rapidly improving as the Kiwis worked up to clear fourth in a tiring field, while still being one second back from USA's Grace Luczak and Felice Mueller, who had fallen behind the Danes in Hedvig Rasmussen and Anne Andersen.
Knowing they just had to go, Scown and Behrent's stroke rate was now the strongest of the boats, and it showed in a very good push to the 1500m mark as they had the speed to make the Americans drop off, but were still trying to get up to Rasmussen and
Andersen, while Glover and Stanning had the best seat in the house to watch from afar.
It appeared all done and dusted as the dominant Brits extended their advantage to over 4s, while the Danes focused on seeing off the Kiwis, who were now only 0.47s behind them.
But caught up in their private war, both second and third lifted their stroke rate as Behrent extolled Scown that even though they had been giving 100 percent since the opening quarter, it was now time to actually go hard - the mental trickery a top athlete must put themselves through at crunch time.
In a final dig, both Denmark and New Zealand began snapping at the ankles of the British boat, with the favourites finally beginning to look mortal as the intensity increased entering the red buoys of the finishing lanes.
Yet the Danes had fired their last shot as Scown and Behrent pushed ahead of them within a few strokes - getting the end of their Black Boat right up to the seats of Glover and Stanning as they crossed the line in 7m 18.29s, with the Kiwis 1.24s behind and a further 1.18s ahead of the Danes.
Behrent spoke with pride about their comeback.
"From 500m to go, I said to Rebecca, 'we've got to go now, we just have to wind it [up].
'So, I think, jubilation that at first we finished and then had that silver."
Scown has upgraded her London 2012 bronze medal with former partner Juliette Haigh, and more than justified Rowing NZ's faith in her and Behrent to take over the pairs boat from fellow Whanganui competitor Kerri Gowler and partner Grace Prendergast last year.
"It means everything. I've been working hard since London, so it's four years of solid rowing, training, effort," Scown said.
"You know, you put so much into it. Not everyone comes away with something to show for it.
"So to get this, and win a medal is incredible for us."
It was to be another quick turnaround for the pair, who would join Gowler and Prendergast and the rest of the women's eight to compete in their final yesterday morning NZ time.
Both said they had plenty left in the tank and would enjoy an afternoon's rest, as the truncated schedule due to weather disruptions at Rodrigo de Freitas meant they had spent a week going from one boat to the other.
"Normal training for us is we thrash it out it two or three times a day," said Scown.
"So having one race a day, one training, it's hard, solid racing but we can handle the load."
Unfortunately, there would be no more fairy tales as the women's eight, at their first Olympics, would finish a very creditable fourth in 6m 5.48s.
The positions did not change much over the 2000m as the dominant American boat went to the front and kept it, winning in 6m 1.49s, with the Great Britain crew claiming silver, narrowly ahead of Romania for bronze.
The Kiwis followed them all home, comfortably clear of the Canadian and Netherlands crews.
Looking ahead to Tokyo 2020, decisions will now have to be made whether 33-year-old Scown will look to carry on with coxless pairs or perhaps just specialise on being stroke for the women's eight, and whether 22-year-old Gowler can move forward with Prendergast or another partner and take over that medal-winning legacy.