The Book of Daniel is narrated by Daniel Isaacson, the son of famed liberal parents who were executed by the American government on a conviction of espionage. The Isaacsons are modeled after the real-life couple, the Rosenbergs, whose 1953 conviction and electrocution captured the public’s interest and has since become a seminal example of how the anxieties, fears, and prejudices during the Cold War era resulted in brutally oppressive measures against its citizens. Daniel is a graduate student at Columbia University in 1967; the narrative that unfolds in The Book of Daniel is actually his dissertation which he plans to submit to his advisor upon completion. The narrative is comprised of many different styles of content: the contemporary events of 1967; memories of his childhood and familial history; and his parents’ arrests, trial, and execution. Daniel leaps back and forth from contemporary to past events. The untraditional narrative also includes letters, newspaper articles, historical scholarship, etc. In some areas he has to piece together what he thinks his parents might have said or thought as he was not actually present. The novel does not follow a logical, chronological progression, sometimes leaping from 1967 to the 1950s multiple times within a given section. For the purposes of the summary, it is useful to consider the two timelines - the 60s and 50s - separately.
The novel begins in 1967. Daniel is a graduate student married to Phyllis with an infant son, Paul, the namesake of Daniel's father Paul Isaacson. On Memorial Day, the family hitches a ride to an institution where Daniel’s sister Susan was taken after a suicide attempt. They meet Daniel's adoptive parents Robert and Lise Lewin, who took in the Isaacson children after their parents were executed for espionage.
Daniel is revealed to be a young man quick to anger, wickedly intelligent, disdainful of others, and an adherent of a leftist ideology like his parents. He also reveals a perverse, sadistic streak in the way he treats his wife and child. Daniel is writing his dissertation - the recounted facts that appear in the novel - as a way to come to terms with the family legacy and perhaps discern his parents' guilt or innocence. While his sister remains at the institution, he visits an East Village radical named Artie Sternlicht and hears from him not only how he plans to overthrow the U.S. government, but how Daniel’s parents actually set the Left’s cause back. At one point Daniel sneaks into the asylum and holds her lifeless form in his arms, distraught over her resemblance to the eternally mute creature of the starfish. Later that year as he continues to delve into the history and incidents of the trial, he visits the wife of the family lawyer, Jacob Ascher, talked with a reporter, and questioned his adoptive father heavily on the details of the Isaacson case.
In October of 1967 Daniel takes his young family to the march on the Pentagon, where Daniel embraces his familial legacy and joins in the clashes with police. At Christmas, Daniel flies to Southern California to try to talk to Selig Mindish, a former family friend and the man whose testimony helped convict his parents. Linda, Selig’s daughter, grudgingly takes Daniel to Disneyland to meet her father. To Daniel’s surprise, Mindish is senile and does not remember anything of the past. However, Mindish does recognize Daniel's face and kisses his forehead in a symbolic gesture of closure. At the end other, Susan succumbs to her suicide attempt and is buried. Daniel returns to complete his dissertation, but is interrupted by the Columbia University student uprising. Daniel is told by a fellow student to close his book and come outside; Daniel obeys, and with a quote from the Old Testament Book of Daniel, concludes his narrative and joins history.
Interwoven in the events of Daniel's life in 1967 are facts and stories of his parents' youth and eventual execution that are fabricated by Daniel himself through memory, evidence, and inference.
Daniel’s grandmother immigrated to America when she was young. Her daughter Rochelle married Paul Isaacson and the couple had two children. Both were ardent members of the Communist Party. Paul owned a small radio repair shop; even though his parents were poor Daniel remarked upon their furious pride, passion, and intelligence. When Daniel and Susan were young, the American government began its clampdown on perceived subversive and leftist views. The Cold War climate of hysteria and anxiety led to the arrest of family friend Selig Mindish and the beginning of frequent FBI visitations to the Isaacson family home in the Bronx. Eventually Paul was arrested on suspicion of espionage, and was followed not long after by Rochelle. Daniel and Susan were sent to live with their Aunt Frieda at first, but the children found her unpleasant and her home miserable. The family lawyer Jacob Ascher then placed the children at the Shelter in the Bronx. Daniel adjusted as well as he could but young Susan was poorly-behaved and spiteful because she viewed the Shelter as prison. Daniel and Susan eventually ran away from the Shelter to try and find their childhood home, but when they arrive it is completely empty. They were placed with a new foster family, the Fischers, which also ended disastrously. Their final placement with Ascher's associate Robert Lewin and his wife Lise is more successful; the Lewins’ middle class home was comfortable, loving, and civil. During this time Paul and Rochelle are housed in separate prisons while trying to secure an acquittal in court. Rochelle was much more self-possessed and reserved while Paul became more crazed and could not believe what was happening to them. The children visit their parents for the first time an entire year after their arrest and are scared by what they find. The Isaacsons are not acquitted, however, and were sentenced to death by electrocution. Their funeral was a large, well-attended event that in the narrative is conflated with Susan’s funeral.
During their teenage years, Daniel and Susan did not get along as well, given the torment and turmoil of their childhood. Susan was very exhibitionist and wild, flaunting her seemingly-improbable combination of innocence and sexuality. Daniel and his sister never talked about their parents while they lived with the Lewins. Susan immersed herself deeply in radical politics and was committed to upholding the family legacy and name by using her trust fund to create a freedom foundation. Daniel’s reluctance to match her levels of enthusiasm and radical activity led to frequent altercations between the siblings. Their last brutal fight predicates Susan's suicide attempt, which leads into the events of 1967 charted throughout the novel.