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The 24-year-old had the worst possible start in the penultimate race of the series in Italy during the weekend.
Another rider cut in front of her and she lost her balance, clipped the back of another rider’s bike and thumped into the turf.
But fans were in for a special treat from the Palmerston flyer.
She picked up her Kawasaki KX250 and rode the way only she can.
Duncan made her way from the very back of the field by taking the tough lines into corners, making double jumps and bold passing manoeuvres.
Duncan passed Papenmeier on the last lap to claim an extraordinary win — her fifth of the season.
That gave her a useful five-point buffer going into the final race. Duncan rode a smart race to finish third.
That left her tied with Dutch rider Nancy van de Ven on 207 points at the top of the standings.
But Duncan was crowned champion because she had more race wins.
"I’m so speechless," the two-time champion said in an emotional post-race interview.
"It’s been just such a difficult year for me.
"That huge crash in Mantova [in September], to get back to my bike and see my handlebars bent. I just thought no, is this championship done?
"But I kept believing and when the times got tough, we kept going.
"I have to thank my whole team, everyone that supports me."
The Women’s World Motocross Championship was delicately poised going into the last round of races.
Just four points separated championship leader van de Ven (166 points) and Duncan (162), while Papenmeier (160) and six-time winner Kiara Fontanesi (156), of Italy, were firmly in contention.
Duncan’s rivals van de Ven and Fontanesi also went down in the crash on the first corner of the first race.
“The start was terrible and I went down.
"Thankfully, a couple of the others went down as well.
"It was such a crazy race. I’ve got to thank my team in the pit box — they were keeping me on it, letting me know how I was sitting.
"Definitely proud of how I stayed composed out there in that situation."
Duncan did not have the best start in race two, either. She was fifth at the first corner.
The track had deteriorated and Duncan adopted a cautious approach, which was in stark contrast to her early effort.
Her moves were more calculated and she was more patient.
She had got up to second but dropped to third place when Fontanesi slipped past after a six-lap battle.
But Duncan held her position to finish third and claim the championship title.
Van de Ven had to settle for the silver medal and Papenmeier claimed bronze.
“It was so close. Coming into the final round, all the girls were riding really well.
"Thankfully I got that first race win, because Nancy and Kiara were on it in the second one and set a really good pace.
"I’m so grateful. I’ve had a lot of tough times and to come through and get this championship, it feels really good.”
Duncan, who grew up in Palmerston, will return to New Zealand next week and begin a two-week quarantine.