The movie opens in 1918 with Tom Sherbourne (Michael Fassbender) traveling by boat to a remote village off the coast of Western Australia. He has accepted the temporary position of lighthouse keeper on the island of Janus Rock. Janus Rock is a small island linked to the mainland, and only visited by boat four times a year by the shopkeeper, Harry, who brings grocery orders, supplies and mail. Because of Janus Rock's remote location and isolation, it was a difficult post to fill before Tom took it over. The permanent lighthouse keeper will return to his job in six months. Tom is a World War I veteran just back from Europe and is looking forward to the solitude the job has to offer.
He is taken to the island by Harry and Bluey. Later we see him at the lighthouse, doing chores and he seems at peace with the solace. Three months into his post, he comes to town for lunch for a break and sees a young woman (Alicia Vikander) throwing bread to the gulls. They exchange a meaningful and extended glance.
He goes to the home of one of the townsfolk has dinner. When the homes owner, Mr. Graysmark introduces Tom to his daughter Isabel, Tom is very pleased to see its the woman he saw earlier feeding the gulls. During dinner he finds out the two reasons the previous lighthouse keeper, Ferguson is on leave. Ferguson informed the authorities that his wife was signaling passing boats which is not allowed. Someone asked well what was the second reason? Mr. Graysmark says Mrs. Ferguson died two years previously. The impression is that he had a breakdown alone on the island and is in psychiatric care but is expected to make a full recovery. Tom returns to his post at the lighthouse.
A few months later Tom is called into the office of his employer. He is advised the permanent lighthouse keeper leapt to his death from the cliffs. He is then offered a three year position as permanent lighthouse keeper. He accepts.
Later, with flowers in hand, he visits Isabel,s home. Her mother invites him to lunch. He advised the family he will be in town for a few days. When Mrs. asks what he plans to do, Isabel pipes in and says, He has invited me on a picnic tomorrow. Tom looks surprised but pleased.
While on their picnic, Isabel peppers Tom with questions but he is very reserved. He doesn't like to talk about the past or the future but she seems enamored with him regardless. Toms mother is deceased and he and his father did not have a good relationship. But his fathers sternness did serve to help him in the war. Isabel tells Tom she has lost both pf her brothers in the war. She tells Tom there is a name for someone who loses a spouse but not a name for a parent who loses a child.
When Isabel asks to visit the lighthouse, Tom advises her its against the Commonwealths laws as only the lighthouse keeper and his wife are allowed one on the island. Isabel says, well marry me. Tom says "you'd have to have rocks in your head to want to marry me". She asks him to write her and he says of course he will.
Over the course of the next few months, the two correspond and fall in love. When Tom proposes via one of these letters, Isabel accepts. Tom promises to always take care of Isabel and to love her forever.
The two have a beautiful wedding and return to the lighthouse. They are very happy and it is very apparent, they are very much in love. Isabel once told Tom she plays the piano and she is very happy to see a piano in her new home. But Tom tells her it doesn't work and is sorely out of tune.
Isabel soon becomes pregnant. Their days are spent deciding on names and Isabel making baby clothes. The couple is blissfully happy.
One night during a very turbulent storm, Tom has to spend the night in the lighthouse to make sure it remains lit. Isabel asks to join him, but he tells her its safer in the house. She is unhappy but Tom kisses her and advises her she will be much safer at home. While doing the dishes, Isabel begins to bleed and experience labor pains. Knowing its too soon, she tries to climb the lighthouse tower to Tom but collapses. Due to the thunder and lightning, Tom does not hear her screams.
The next morning Tom finds her unconscious and carries her back to their home. The baby is stillborn and the two bury the baby with a cross marker inscribed with the date and always remembered. Tom tells Isabel they can try again. Tom begs Isabel to let him send for a doctor but she refuses. A few days later, she sees a boat approaching and a man carrying what appears to be a medical satchel. She flies into a rage at Tom for betraying her wishes and runs off.
Later, she sees one of the men on the porch and angrily storms into the house. She then sees it wasn't a doctor but a man Tom hired to tune the piano. They kiss and embrace.
Late.r we see Isabel is pregnant again. Over the course of the next few months, her pregnancy advances. One day while playing the piano, she begins to experience bleeding and pain. She screams its too early and pleads with Tom to make it stop. Through his tears, he repeatedly pleads, Tell me what to do! Later there are two crosses signifying this baby died as well. Isabel is extremely despondent and depressed, spending her days lying in the grass next to the burial plots of her babies.
One day while washing the lighthouse windows, Tom sees a rowboat in the distance. At the same time, Isabel hears a baby crying. Using a scope, Tom sees a body in the boat, he screams for Isabel, and they both begin running to the water. They discover a dead man and a baby in the boat.
Isabel takes the baby into the house and feeds and changes her. When Tom comes in, he advises her he must send a message to town. She begs him to wait until morning. This greatly concerns him because it is against protocol be he agrees.
The next day as he leaves to send a message, Isabel runs after him begging him to let her keep the baby. She pleads that no one needs to know. They can bury the body and raise the baby as their own. Tom says no. She tells him it is a victimless crime. He tells her they can report it and ask to adopt the baby. She convinces him no one will allow a child to be adopted by a couple basically alone on an island with no hospitals or schools. She pleads with Tom. With both in tears, they embrace.
Tom buries the body and sends the boat out to see. While pushing the boat out to see Tom notices a silver rattle in the shape of an owl. He places it in his pocket. He then pulls up the last cross from the grave of their second child and sends a message to town informing the baby came early, Isabel is fine and no need for medical attention.
A few months later Bluey and Harry visit with provisions. They congratulate the happy couple and remark on how beautiful the baby is. Bluey notices the rattle while playing with the baby, Lucy.
Lucy grows and flourishes on the island and is a very happy baby. The family visits town and Lucy meets her grandparents. The child is very pleasant and eats with a great flourish to the families delight. Family and friends travel to the vicar for Lucy's christening and while waiting for the vicar, Tom hears a woman singing. He sees a woman (Rachel Weisz) in black leaving flowers on a grave, curious he walks to the marker after she leaves and reads it. It is the grave of her husband and child.
Later, Tom asks the captain about the woman. She is Hannah, the daughter of one of the wealthiest families on the island. She married a German baker (Frank Roennfeldt) and the citizens of the town were displeased due to many losing family and friends in the war. When she tells her father Septimus Potts (Bryan Brown) that she is to marry him, he disowns her. She marries him anyway and the two were very happy. They had a daughter, Grace. One day after being harassed by the townsmen, Frank grabs Grace and jumps into a boat. The two are lost at sea and never found. This occurred around the same time Tom and Isabel found the baby. Tom is devastated. He tells Isabel they must confess what they did. She tells him its too late and the baby is hers. She is her mother. Tom is visibly torn.
Before returning to the lighthouse, Tom writes a letter to the mother telling her the baby is fine but her husband died. He tells her she is loved. Meanwhile, Hannah, her father and her sister Gwen ask the police to search for the baby but he doesn't appear concerned.
Three years past. Lucy is a happy, beautiful child who is worshipped by Tom and Isabel.
On the 40th anniversary of the lighthouse, the family visits town for a ceremony. The Potts family has commissioned an exact replica of the lighthouse for display. Tom turns and sees Lucy's mother. When asked to say a few words, he is too shaken to make much sense and blames it on the surprise of being asked to speak.
Later at the reception, Isabel meets Hannah and is devastated when she realizes who she is. She runs to the ladies room and is sick. Tom again begs her to let him tell the authorities but she refuses him. Later that night Hannah hears her mailbox and inside finds a package containing the owl rattle. Isabel's father suggests the lighthouse is too isolated for the mother and child and suggests Tom leave the two in town for a while. The three are then seen on the boat returning to the lighthouse. Isabel is downcast.
The Potts take the rattle to the police and fliers are placed around town with a reward for information regarding the rattle. We see Bluey reading the flyer.
A few days later a boat is headed to the island. Tom tells Isabel he is sorry, but he had to do the right thing but he will tell authorities it was all his doing. Isabel furiously attacks Tom. The police take Lucy and Tom is thrown in jail. During his interrogation Tom is accused of killing Frank but he insists Frank was already dead. Isabel is questioned and asked if Tom killed Frank. The audience does not see her answer the question. Lucy is inconsolable with her mother. She begs for Isabel and Tom and the lighthouse.
Isabel is released from jail and is seen in bed crying, her mother pleading with her to eat.
One day on a visit to town, she sees Lucy (Grace) in the store with her mother and aunt. Lucy runs to Isabel and her mother repeatedly asks Isabel to give her the child. She takes the child from Isabel as Lucy screams. Isabel breaks down.
Captain delivers a letter from Tom to Isabel and tells her that Tom needs her. She replies so does my baby. She doesn't read the letter but places it in a drawer.
Hannah visits Tom in jail. She asks why they did it. He tells her Isabel is innocent. It was all him.
We later find out Tom is to be tried for murder. Apparently Isabel told the police he killed Frank.
One day Hannah calls Lucy (Grace) for dinner. When she doesn't answer, she searches the house but cant find her. The police visit Isabel's home; she is there, but no Grace. Hannah prays that if Grace is found, she will do what is best for the child. A search of the town begins. Grace is later found asleep near the water. She was trying to find the lighthouse.
Hannah remembers a conversation with Frank when he tells her it is easier to forget a wrong done against you than hold on to it forever. The next day, she visits Isabel and tells her that the right thing may be for Grace to be with Isabel. She tells Isabel that once she testifies against Tom, she will return the child to her.
Isabel's mother tells her that Tom loves her and while Grace also has people who love and care for her, Tom only has Isabel. Isabel finally reads the letter and realizes how much Tom loves her. She runs to the jail, but Tom is already headed to the boat to be moved for his trial. She races to the dock and runs to Tom. He tries to hurry the boat but she confesses that Frank was already dead and it was all her fault. She was the reason Tom kept the baby.
Later, the constable is speaking with Hannah and he tells her Frank was already dead. She asks what will happen to Tom and Isabel, he tells her jail. She asks what if I speak on their behalf. He asks why and she repeats what Frank said about forgiveness. He tells her Tom and Isabel would probably only spend a few months in jail.
Later, Grace and her grandfather are riding a horse and he is telling her about her mothers childhood. When he calls her Grace, she says my name is Lucy. He says "well what if I call you Lucy Grace?" She says that is fine. They find Hannah lying in the grass and she and Lucy Grace bond while making daisy chains. It is clear Lucy Grace is growing comfortable with her mother.
The next scene indicates it is now 1950. In a hospital bed we see Isabel asking Tom if God will forgive her. He says he already has but she just needs to forgive herself. Later, Tom is sitting in his kitchen when he hears a car approaching. A woman gets out with a baby and introduces herself as Lucy Grace. Tom gives her a letter from Isabel. The letter tells her how she stayed away from her as agreed but hopes she would someday find them. She tells Lucy Grace how much she was loved. The letter informs Lucy Grace that if shes reading it Isabel has died but Lucy Grace finally came to find them.
Lucy Grace places the baby in Toms arms. As the baby coos, he tells the baby that Isabel would have just loved him. Lucy Grace asks Tom can she and baby Christopher visit him again, he says he would love for them to. They embrace and Tom closes his eyes and cries.