Birdsong has an episodic structure, and is split into seven sections which move between three different periods of time before, during and after the war in the Stephen Wraysford plot, and three different windows of time in the 1970s Benson plot.
The first stage starts in pre-war Amiens, France. Stephen Wraysford visits and lives with René Azaire, his wife Isabelle and their children. Azaire teaches Stephen about the French textile industry. He witnesses a comfortable middle class life in Northern France alongside industrial worker unrest. Azaire and the significantly younger Isabelle express discontent with their marriage. This sparks Stephen's interest in Isabelle, with whom he soon falls in love. During one incident, Azaire, embarrassed that he and Isabelle cannot have another child, beats her in a jealous rage. Around the same time, Isabelle helps give food to the families of striking workers, stirring rumours that she ishaving an affair with one of the workers.
Stephen's love of Isabelle transforms into a passionate affair. Isabelle confronts Azaire with the truth of their relationship and Azaire evicts Stephen. Isabelle leaves with him, running away to Southern France. There she becomes pregnant, and momentarily loses faith in her relationship with Stephen. Without telling Stephen, she flees, returning to her family home and the one constant in her life: her sister Jeanne. Later, Isabelle's father makes a deal with Azaire for her return to maintain her honour; Isabelle is forgiven but soon regrets leaving her true love, Stephen. However, she does not reach back out to Stephen.
The second section rejoins Stephen, when he is a lieutenant in the British Army at the start of the war. Through his eyes, Faulks tells the reader about the first day on the Somme in July 1916 and the Battle of Messines near Ypres in the following year.
Several episodes depict a downtrodden Stephen whose only respite is his friendship with Captain Michael Weir and his men. Stephen gains the reputation of a cold and distant officer. He refuses all offers of leave, because he is committed to fighting the war.
His story is interleaved with that of Jack Firebrace, a former miner employed with the tunnelling companies of the Royal Engineers in the British trenches to listen for the enemy and plant mines under the German trenches. In one expedition across No-Man's Land, Stephen is badly injured but survives.
During these episodes, Stephen feels lonely and writes to Isabelle, feeling that there is no one else to whom he can express his feelings. He writes about his fears that he will die, and confesses that he has only ever loved her.
Alongside the main story, there is the narrative of Stephen's granddaughter, Elizabeth, who, whilst struggling with her already married boyfriend, Robert, unearths Stephen's journals from World War I and seeks to learns about his experiences at Marne, Verdun and the Somme. She discovers that Stephen's journals are encoded, but tries to decipher them.
Stephen has a chance encounter with Jeanne, Isabelle's sister, while on leave in Amiens. During this encounter, Stephen convinces her to allow him to meet with Isabelle. He meets her but finds her face disfigured by a shell with scarring caused from the injury. Stephen discovers that Isabelle is now in a relationship with Max, a German soldier.
Stephen returns to England briefly, and finds relief at being able to enjoy the Norfolk countryside away from the trenches. When he meets Jeanne again on the way back, he tells her how he dreads returning to the front line after leave. Weir, Stephen's closest friend, is eventually killed by a sniper's bullet while in a trench out of the front line.
Elizabeth continues researching the war and talks to war veterans Gray and Brennan (who knew Stephen) about their experiences. During this period, she also becomes pregnant with Robert's child.
The WWI plot ends with Stephen and Firebrace trapped underground after a German mine explosion; with their way out blocked, they talk and share their experiences, with Firebrace grieving for his dead son John and Stephen telling him of his former love for Isabelle. Stephen finds some explosives and Firebrace, himself close to death, tells him how to lay them in order to blast their way out of the tunnel. Before Stephen completes the task, Firebrace dies. The explosion successfully clears a way out for Stephen, and he is rescued by Levi, a Jewish German soldier, as the war ends.
Elizabeth finally decides to reveal her pregnancy to her mother Françoise, who, to Elizabeth's surprise, is supportive. Over dinner, she learns her mother was raised by Stephen and Jeanne, who married and settled in Norfolk after Elizabeth's grandmother Isabelle's premature death due to the postwar influenza epidemic. Elizabeth and the still-married Robert go on holiday to Dorset, where she goes into labour and has a son, naming him John (after Jack Firebrace's late son). The book ends with Robert walking down the garden of the holiday cottage and having an immense sense of joy.