Spoilers Alert, Spoilers Alert: the text reveals key parts of the plot.
The story is divided in three parts: the first takes place in the exact day of September 11th. The second part takes place from November 21 to November 24. The third part takes place on early November 24th. There is an epilogue, taking place in December 1st, 2001.
First part takes place Tuesday morning, 11th September 2001. In Boston, Jane and Daria drive Quinn to the Airport, for her to take the plane back home to Lawndale. It is revealed that Daria and Jane are attending their college freshmen year, Jane having been able to enter in the fall semester instead of the winter one, and that Quinn had been attending a conference on alcoholism and staying in Daria's dorm room.
Quinn is left at the Logan airport and Daria and Jane drive back to the University campus, where they are horrified to learn about the hijackings and crash of the planes. They try unsuccessfully to call Quinn and eventually find out that she hadn't board any plane. Extremely relieved, they pick up Quinn at a nearby hotel, where she appears shell-shocked.
The second part takes place some weeks later. Daria and Jane fly back to Lawndale for thanksgiving. When they arrive, they receive shocking news: Jane's parents had divorced and sold their house, forcing Jane to stay in Daria's home; Trent makes some distressful revelations regarding the Lane's family; and Daria discovers that Quinn is still in shock, and almost lifeless, a shadow of her former self and with an appearance several degrees below Fashion Club Standards. The days are plagued by discussions between Jane and Trent, visits from the FBI and tense moments between Daria and Helen, that warns her to leave Quinn alone, despite Daria's protests. Daria is unable to reach her sister.
The third part takes place during the night. Jane, woken up in the middle of the night, discovers Quinn's room empty and a suicide note. Horrified, she and Daria rush to the water tower, were Quinn had hinted she had been some time before. There, they discover Quinn wanting to kill herself. She eventually reveals to Daria the cause of her distress: during the September 11th attacks, she had found a boarding pass of a little girl, stayed with her, and helped reach her plane, only to discover it had been one of those hijacked and destroyed, killing everybody in it. Daria is able to reach for her and save her, though she herself falls and is severely injured in the process.
The Epilogue takes place a week later, December 1st. Daria is still injured and has casts. She and Jane are to be driven to Boston by Trent. Quinn is much better and lively, and both sisters share a warm goodbye before they part.
The flight referenced in the story could have been either American Airlines Flight 11 or United Airlines Flight 175, which departed from Logan International Airport in Boston, and which crashed into the North and South Towers of the World Trade Center.
"Nine-Eleven and Counting" - the story at TAG's website.