But he was soon attacked by Brent Mangos, driving second favourite Five Card Draw, and knowing how aggressive Mangos can be, Thornley relented. It seemed the right move.
"I know how much speed this horse has and I thought if Five Card Draw stayed in front then we would outsprint him up the passing lane."
But then Mangos decided to pull a tactical move which should have taken Franco Nelson out of play.
He, in turn, handed the lead away to Mista Mara and that left Franco Nelson locked away three deep, where Thornley thought he might still be at the finish line.
"When that happened I was dreading the next 1000m," said Thornley. "I knew there was a chance Mango could do that but Five Card Draw being so good, I thought he'd stay in front."
Mangos's move was the right one and should have been lauded as tactically brilliant.
But then the race was turned on its head again. When a rival outside him galloped, Franco Nelson was able to ease off the markers and into the one-one, a few strides before Five Card Draw broke stride and lost valuable momentum.
All of a sudden, in a crazy few seconds, Franco Nelson has gone from likely winner, to hard-luck story to being the horse to beat again.
From there the result was never in doubt as he strode to his career biggest win, with Arden Rooney holding on for second in front of Mista Mara, Five Card Draw regathering himself for fourth.
"It was pretty wild out there, it was like a junior drivers' race," said Thornley.
"I thought I might have stuffed it up but I always had the possible ace up my sleeve of having so much speed to get me out of trouble. But I really didn't see it going like that."
The win confirms Franco Nelson as the current top dog in a crop of horses that has also seen Alta Christiano, Border Control, Bit Of A Legend and Five Card Draw lauded as the best of the best.
Franco Nelson won't get the chance to put his case forward again until next year.
"He is off for a spell now. He is not eligible for the Sales Series race at Alexandra Park next month so he can have a break and get ready for the Derbys."
The win capped a wonderful training performance from trainer Steven McRae, who has not only picked Franco Nelson up after an arduous Australian winter campaign but got him over recent allergies.
While beaten, Mangos was still happy he had done the right thing.
"He is actually a better trailer than a leader and putting Franco Nelson three deep made sense. "But I have no idea why he galloped and that is when things came unstuck for us."
Regardless, with the rivalry that pair are just establishing and the other superstars still to come back in this crop, this is going to prove a tough season to win a Derby.
Sires' Stakes Final
* Franco Nelson win a tactical Sires' Stakes Final at Addington.
* His driver Craig Thornley thought he has made a crucial error.
* He will now be spelled and be set for the Derbys.
