A Fall of Marigolds focuses on two characters living in the New York City area separated by 100 years (1911-2011) but linked by traumatic events. The characters' storylines will be discussed separately in this plot summary to keep their stories linear, though they converge in the end, as will be discussed. Both characters' stories are written in the first person in past tense. The novel does include several sections in both Taryn and Clara's narrative where the characters remember past events. These passages are also written in the past tense.

The novel opens with Taryn Michaels in September 11, 2011. Taryn, a textile restorer, notes how she was bewitched and haunted by a scarf with a pattern of marigolds that she only saw for one day, September 11, 2001. Taryn lost her husband in the September 11, 2001 terrorist attacks, a loss she has never processed but was reminded of when a photograph of her and a florist from that morning was published in a magazine to commemorate the ten year anniversary of the attacks.

Throughout Taryn's chapters she reminisces about the attacks and that morning and about the guilt she feels for her husband's death. She had been set to meet him that morning at the restaurant on the top floor of one of the buildings. She was going to tell him she was pregnant, a fact she had waited to tell him. She was in Lower Manhattan that day to meet a wealthy client who wanted a copy of a marigold scarf. When she got out of the building, Clara was shocked at the chaos outside. She asked a man, Mick Demetriou, to use his cell phone to try to get through to Kent since she had forgotten her phone at home. Mick said sure, but Kent did not answer her texts. Mick stayed with Taryn for much of the morning but they were separated at one point.

Ten years later, Taryn heard from Mick, who called her at the florist shop to say that he has her scarf, which she left near his van, and he wished to return it to her. Taryn was initially cold to Mick but eventually relented and joined up with him. They helped each other process the trauma of the day and became friends. Mick showed her a text from Kent asking him to tell Taryn to "Be happy."

Taryn tried to return the scarf to its owner, but the woman asked her to keep the scarf since it meant more to Taryn than it does to her. She showed Taryn a letter from Clara Wood to her aunt in which Clara gave the scarf to her aunt to help her move on from heartbreak, telling her to be happy. Taryn realized that the message all along was that she had control over her life and had free will to choose who she loved even if it turns out badly.

Interspersed with Taryn's chapters are Clara Wood's. Clara was a nurse working on Ellis Island in September 1911. Clara came to the island after experiencing a heartbreaking loss in the Triangle Shirtwaist Factory Fire in Lower Manhattan in March of that year. Clara had met a man, Edward Brim, in the building when she worked as a nurse in a clinic there. Clara fell in love with Edward and believed he loved her, too. He asked her to meet him on the ninth floor so he could show her the factory, but there was a terrible fire and he perished when he jumped from one of the windows. Clara went to Ellis because it was an "in-between place." There she made friends with her roommate, Dolly.

One day a Welsh man was admitted to the hospital. He was wearing a marigold-patterned scarf and asked Clara to save his wife's things from the incinerator. The man, Andrew Gwynn, had lost his wife, Lily Ravenhouse Gwynn, to disease on the passage over to America. Clara discovered a certificate of annulment and realized that Lily had meant to abandon Andrew when they got to New York. Lily had been married to another man, Angus Ravenhouse, who was horrible and she was afraid he would hurt her. As the story progressed, Clara realized that Andrew and Lily married in haste. Lily's deceit haunted Clara, and she decided not to tell Andrew about it.

Meanwhile, a new doctor, Ethan Randall, joined the staff. He took a liking to Clara and had a crush on her. Ethan and Dolly were concerned about Clara's growing attachment to Andrew, even wondering if it was inappropriate. Clara agreed to change wards. They discussed poetry one night. He accompanied her to Manhattan to meet her father, who told her of a job offer for her to accompany a man and his ailing wife on their trip to Scotland. That same trip to Manhattan, Clara looked up Edward's obituary and realized that he was engaged at the time of his death. Furious, Clara took the ferry back to Ellis and discovered that Andrew, who had been discharged that day, did not take Lily's scarf and letter with him when he left. Clara had given it to Dolly to give to him, but he gave it to Clara as a memento.

Clara, determined to leave Ellis, traveled back to her home in Pennsylvania and accepted the traveling nurse position. Back on Ellis, a detective came looking for Andrew saying he had stolen a valuable necklace from Lily and the Ravenhouses. Clara traveled to Manhattan on her own and found Lily's necklace in a trunk in a boarding house room she had rented. She then tracked down Andrew's brother, Nigel, and read Lily's letter to him and to the detective who arrived at the same time. She left and waved to Andrew from a trolley car. She went back to the newspaper and read about the fire, learning that Edward's fiancee had already married someone else. Clara then went to Edward's parents to tell him that he was a hero for jumping out of the building with a young girl during the fire. She left a letter telling them this, and then she went to his grave, telling him, "Thank you."

Clara returned to Ellis and realized that Ethan was in love with her. She told him she needed time before she could love again. He kissed her and they walked back to the building together. From the letter that Taryn read in the final chapter, the reader learns Clara's fate; she took the traveling nurse position but left it early to return to New York to be with the man who loved her and who she loved, presumably Ethan.