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After a winless streak spanning more than two years, the former world number one looked set to break her duck heading into the final round at the Highland Meadows Golf Club, having led the field over the first three days.
Ko held a five-shot lead going into the final six holes, but stumbled to bogeys at the 14th and 16th followed by a horror 18th – a par 5 considered to be the easiest hole of the course – where she double bogeyed to hand the tournament to in-form American Danielle Kang.
"It's tough," Ko said after her round. "Obviously, not the finish that I had envisioned but Danielle played great today. Every time she made a mistake she fought back with a birdie, so credit to her.
"It's not like she played mediocre and I played mediocre. She played good golf.
"Obviously I would've loved to be the one holding the trophy, but I think if somebody said, 'Hey, you're going to be second at Marathon coming into the stretch', I would've been, 'okay, cool. I would take that'."
Ko still had a one-stroke lead over Kang heading into the final hole of the day, but capitulated on the par 5 18th in one of the most brutal golfing meltdowns since Jordan Spieth at the 2016 Masters.
After a solid shot off the tee, Ko found the cart path with her second. She then hit the rough on her third and found the bunker in her fourth – the worst shot of them all – after her chip from the edge of the green rolled back down the slope and into the sand. By the time she made the green, Kang had already made par and Ko missed the putt to send the tournament to a playoff.
Ko said the 18th was "God's way of telling me it wasn't my day".
"With the ground being pretty firm it was going to be a risky shot either way," she said of her final hole.
"You know, maybe now when you look at it, maybe I should have hit the higher shot in."
Ko won 17 LPGA titles and two majors during her sensational rise from teenage prospect to world number one, a title she held for 84 weeks.
However, a rough patch of form and mental struggles, as well as a host of coaching and swing changes left the 23-year-old without a win in 27 months.
Despite coming so heartbreakingly close to the breaking her streak, a graceful Ko said she's not going to dwell on her disaster finish and wants to take the positives into the rest of the season.
"Yeah, you know, I think I have to see the positives," she said. "I'm pretty sure I'm going to be disappointed and go, 'Oh, man, I should have done this over that'. But when you look back at everything and you take everything apart, you're going to have so many things to like think so negatively about.
"But I think there are so many positives from the week, and I feel overall like more confident in my game. I think that's really the goal I had coming into this stretch after quarantine."
She said she won't let the result stop the progress she's made over the last week, where she started to gain confidence in her game once again.
"I felt like throughout the week I was getting more and more confident in my game.
"Like today I felt like I hit the ball pretty good. Like the only real missed shot was the tee shot on 17, and it really wasn't so far off. I was so surprised how far it actually had run through.
"Other than that, there were no like real errors. Maybe some course management errors. But my short game wasn't like that good, like making up and down throughout the week, so I think here and there I could have picked a few shots through that."
Ultimately, Ko said it was "nice to be able to play some solid golf after this long break", and looked forward to playing more golf.
"To see putts drop this week is nice. I think when you see that you get more and more confidence. I feel like that's what has been building the last couple weeks. So I'm planning to play five weeks in a row."
Kang, who took out her second straight win at the LPGA Tour, said she almost gave up hope going into the final stretch of the day.
"To be honest, when I was five down, that three putt [on the 12th] really bothered me." Kang said.
"My caddie looked at me and said 'you're still right in it' and I said 'I'm five down, I'm five back.'
"He said 'there's six holes to go and five down,' and I kind of liked that mentality.
"I kind of went into a matchplay mode mentality for that one, definitely made some good birdies coming in and kept it together."