The U.S. athlete was hoping to finally "make peace" with the Boston Marathon, which she was forced to forfeit past year due to a bone fracture in her lower back.
Flanagan, despite the conditions, still managed a top-10 finish herself (ending up seventh in the women's race).
The Arizona State Sun Devils said it best: Chills.
"It's storybook", Linden told NBC Sports of her win.
Desiree Linden celebrates after winning the women's division of the 122nd Boston Marathon on Monday.
Michigan's Desiree Linden won the 2018 Boston Marathon on Monday, becoming the first American woman to do so since 1985.
"I nearly feel like I have to pretend like I don't want to win it in order to do well", she said.
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According to USA Today, the 34-year-old athlete from MI displayed incredible sportsmanship before claiming her title by actually stopping to wait for Flanagan a couple of miles into the race.
Her unofficial time was 2 hours, 39 minutes, 54 seconds.
'It's supposed to be hard, ' said Linden, who wiped the spray of rain from her eyes as she made her way down Boylston Street alone.
Linden's run was a memorable one not only for her triumph over the conditions, but also for her sportsmanship displayed on the course.
Lisa Larsen Weidenbach's 1985 victory was the last for an American woman - before the race began offering prize money that lured the top global competitors to the world's oldest and most prestigious annual marathon. Fellow American Sarah Sellers crossed the finish line in second place.
"I don't have the right words", Linden told reporters.
Japanese runner Yuki Kawauchi won the men's title Monday, winning his fourth marathon this year and earning Japan's first Boston Marathon win since 1987. Canadian athlete Krista Duchene finished third, at 2:44:20.