It's ten years after the birth of Dane, and Meghann "Meggie" O'Neill (Amanda Donohoe) is forced to run Drogheda basically on her own, since all her brothers went off to fight in World War II. To make matters worse, a two–year drought has struck the area. One day, Meggie's estranged husband, Luke, arrives on Drogheda and begs forgiveness. Meggie, lonely, in need of a man to run the ranch and to be a father for her children, reluctantly takes Luke back, and she becomes pregnant once again.
Father Ralph de Bricassart (Richard Chamberlain) decides to become a full-time priest to fulfill his deep love for God. He has been using his church in Rome as a haven for Jewish war refugees. After Ralph uses some of Mary Carson's estate money to send a young orphan to America, the church "punishes" him by forcing him to return to Drogheda to guard the church's bequeathed property and to convince the Australian government to accept more refugees.
Father Ralph arrives in Australia unannounced and Luke is not pleased to see him. Luke demands Meggie move with him immediately to a ramshackle cabin on the farm he purchased, just to get Meggie away from Ralph. When Meggie resists, Luke strikes her, causing her to miscarry.
Meggie decides she can never return to Luke, but Luke declares he only returned for Dane, whom he thinks is his son. Meggie takes Luke to court for custody of Dane. The judge, a Protestant biased against Dane's desire to be a priest, awards custody to Luke, with Meggie refusing to ruin Ralph by announcing Dane is his and not Luke's son. She decides to avoid scandal, confronting Ralph with the fact that he loves God more than her, that he will always be devoted to a greater good. She has raised her son without the knowledge of who his father is.
The rains finally come, and Ralph and Meggie do their best to round up the animals before the flood comes. Unable to make it back to Drogheda in the downpour, the two find refuge in a small cabin, where a night of romance ensues.
Meggie's mother, Fee, in a last-ditch attempt to reclaim Dane, confronts Luke with the truth—Dane is not his son but the son of Father Ralph. Luke swears never to reveal this fact for fear of losing Meggie and his children to Ralph forever.
Luke confronts Ralph and starts a fight, declaring if Ralph can beat him he can have Dane. Ralph defeats Luke, and torn and bleeding, Luke returns Dane to Meggie.
The Missing Years was generally panned by critics and fans of the original miniseries for being unfaithful to the book. Adding to the dismay was the fact only one actor, Richard Chamberlain, returned to reprise his role as Ralph de Bricassart from the original miniseries.
In the original The Thorn Birds Dane, at age 17, shocks Meggie and Father Ralph with his desire to become a priest. In The Thorn Birds: The Missing Years, Dane talks about little else at age 10.
In the original, Meggie's mother, Fee (played by Jean Simmons), is a deliberate, slow-talking, aristocratic woman who "lost faith in her church", while in the "Missing Years," Fee (played by Julia Blake) is a religious, rapid-talking gossip-bearer.
Luke turns from a drunken womaniser who hangs around his mates all day to a loner who lives by himself on a farm.
Father Ralph offers to leave the church and marry Meggie, something that he never implied in the original. She finally gets the love she was hungering for, and Father Ralph breaks his vow of chastity.
Meggie has two surviving brothers in the original: Jack and Bob, while in the "Missing Years" Frank and Jack are mentioned.