REUTERS/Jim Young
The investigation was reopened after investigators found potentially relevant material on a computer belonging to Abedin's estranged husband, Anthony Weiner.
Weiner, a former congressman from New York, was under FBI investigation for sending inappropriate messages to a teenage girl. (He pleaded guilty to the charges in May and Abedin filed for divorce shortly thereafter).
Clinton wrote in "What Happened" that Abedin "looked stricken" after hearing the news and burst into tears.
"Anthony had already caused so much heartache. And now this," Clinton wrote.
"This man is going to be the death of me," Abedin, who first worked for Clinton as a 19-year-old intern in the 1990s, said as her boss hugged her.
Clinton, who played a role in introducing Abedin to Weiner in 2001, defended her decision to stick by her aide, whom she's described as a surrogate daughter.
"After more than twenty years working with Huma, I think the world of her, and seeing her in such distress broke my heart," Clinton wrote. "In the days that followed, some people thought I should fire Huma or 'distance myself.' Not a chance. She had done nothing wrong and was an invaluable member of my team. I stuck by her the same way she has always stuck by me."
Upon first reading former FBI director Jim Comey's October letter notifying Congress that the FBI was reopening its investigation into the private email server she used as secretary of state, Clinton said she thought it was "a bad joke."
Comey had closed the investigation on July 5, 2016 and was widely condemned for notifying Congress of its revival, a move that many condemned as a breach of FBI protocol, which prevents prosecutors from commenting on investigations before charges are brought.
"The FBI wasn't the Federal Bureau of Ifs or Innuendoes. Its job was to find out the facts," she wrote. "What the hell was Comey doing?"
Clinton said she recognizes that re-examining the ways she believes she was wronged by Comey during the election won't change things.
"It wasn't healthy or productive to dwell on the ways I felt I'd been shivved," she wrote.
But she added that it was "incredible to see Comey go from villain to martyr in five seconds flat" after he was fired by Trump in May, ostensibly for his mishandling of the investigation into Clinton's emails that Trump had once praised him for.
"I read Rosenstein's memo in disbelief," Clinton said of Deputy Attorney General Rod Rosenstein's recommendation to Trump to fire Comey. "Here was Trump's number two man at the Justice Department putting in writing all the things I'd been thinking for months ... It was as if, after more than two years of mass hysteria, the world had finally come to its senses. But the story quickly fell apart."