Returning to Jerusalem for a homecoming after seven years, Judah enters his neglected and overgrown home. In the shadows he sees Esther, startling her when he identifies himself: "Esther, it's Judah." She cannot believe he is alive. He learns that her father, his old steward, Simonides, was imprisoned and nearly killed by Roman torture. Ever since then, they have been living there in hiding as recluses. Simonides explains how he has overcome his handicap by introducing Malluch (Adi Berber):

Do not pity me, Master Judah. In fact, I'm twice the man I was. There's Malluch, my other half. We met in the dungeons at the citadel We were released on the same day, Malluch without a tongue and I without life in my legs. Since then, I have been his tongue and he has been my legs. Together, we make a considerable man.

Esther had never given up hope that Judah would return. Simonides has not only saved the family fortune but increased its wealth. Judah's main purpose in coming back, he explains, is to find his mother and sister, but there is no word on them and they are presumed dead after four years in the dungeons.

Judah and Esther are reunited when they speak to each other in the upper balcony: "We stood here before, a long while ago." They recall their words to each other, and Esther admits that she is not a bride. They embrace and kiss, and Judah shows her the ring he had pledged to wear until he met the woman he would marry. Esther realizes he still carries revenge and hate toward Messala in his heart:

I've seen too much what hate can do. My father is burned up with it. But I've heard of a young brother who says that forgiveness is greater and love more powerful than hatred. I believe it.

She cautions him to keep away from Messala, concerned that this time, he may die.

The next day, Messala is interrupted in his home during whip practice - he is brought a gift from the son of a Roman consul, champion of the great circus in Rome. He is amazed at the generosity of a stranger: "It's magnificent, and from a man I've never met." Judah corrects him: "You're wrong, Messala." Judah explains his magical transformation: "You were the magician Messala. You condemned me to the galleys. When my ship was sunk, I saved the consul's life...Now I've come back, as I swore I would."

Judah then boldly confronts him and asks about his mother and sister, threatening: "Find them Messala! Restore them to me, and I will forget what I have vowed with every stroke of that oar you chained me to." He demands that Messala trace his loved ones and learn whether they are still alive in prison. Judah will return the next day for the news: "Don't disappoint me, Messala." An aide is dispatched to the citadel to find out and is horrified to find that they have contracted leprosy after years of being kept in solitary confinement deep in Roman dungeons. Miriam and Tirzah are ordered to be freed, but moved as outcasts to the Valley of the Lepers, outside the city.

On their way, released in tattered rags from the dungeons, they visit their home and are spotted hiding in the garden by Esther. She wishes to embrace them but is told: "We are lepers." They ask: "Is Judah living?", learning that he is alive too and is searching for them. They forbid Esther to tell Judah, pleading with her:

He is never to know. Let him remember us as we were. There's nothing else I can hope for, only this.

After they leave, Esther covers up for them as she promised, telling Judah: "They were dead...in the prison, when I was waiting for news of my father...Oh Judah, you have come to the end of your search. It's over now...Judah, Judah, forget, forget, forget Messala. Go back to Rome." Judah is distraught and anguished.

In the Roman baths, the sheik promotes the upcoming chariot race, taunting the Romans by wagering with "no limits" his entire fortune, a thousand talents. The Prince of Hur has agreed to compete against his bitter rival by driving the Sheik's chariot with four beautiful white horses. The Roman tribune Messala accepts the four to one betting odds against the Jew. Ben-Hur seeks vengeance by shaming and defeating Messala, and the Sheik by bankrupting him. At the Sheik's camp, Ben-Hur trains, practices, talks strategy to the horses, and develops a loving relationship with them.

The charioteers make preparations for the race. Before the race, Judah prays at a wall in which there are three nails: "God forgive me for seeking vengeance. But my path is set and into your hands I commit my life. Do with me as you will." The Arab sheik presents Judah with the Star of David to wear during the race: "The Star of David, will shine out for your people and my people together and blind the eyes of Rome."

As they enter their racing positions, Messala warns: "This is the day Judah. It's between us now." Ben-Hur's chariot is pulled by beautiful white horses, Messala's by four, glistening black steeds. Messala has outfitted his chariot with revolving blades at the end of each axle, effective in chewing the spokes of the wheels of other chariots. Before the memorable and spectacular 11-minute chariot race scene, the charioteers parade around the ring in a display of pageantry. The setting is majestically impressive with a central divider strip composed of three statues thirty feet high, and grandstands on all sides, rising five stories high. Pontius Pilate greets the audience with some opening words: "Citizens. I welcome you to these games in the name of your Emperor, the divine Tiberius. We dedicate them to his glory and to the glory of Rome of which you are all part." The throng of people gathered to see the race is huge, cheering drivers from Alexandria, Messina, Carthage, Cyprus, Rome, Corinth, Athens, Phrygia, and Judea. The focus of the race is on the two chariots of Ben Hur and Messala - with white and black horses respectively. A crown of victory will be given to the victor - the chariot that first completes nine rounds.

The eager horses and chariots are held back at the starting point until the signal to begin the race is given. The battle between the competitors is highlighted by a series of close ups of the action. One by one, Messala eliminates the other drivers in the ferocious race, shattering their chariots. The climactic ending to the race occurs when the chariots of Messala and Ben-Hur, in hateful rivalry toward each other, run neck-and-neck and slash at each other. Messala tries to destroy Ben-Hur's chariot by moving close with the blades, but as the wheels lock and he loses one of his wheels, Messala's chariot is splintered. He is dragged by his own team, then trampled, and run over by other teams of horses. Defeated, he lies bloody in the dirt, his body broken and horribly injured.

The people of Judea are thrilled by the Jew's victory, and congratulate him during a victory round. Pontius Pilate commends him for "a great victory. You are the people's one true god for the time being. Permit us to worship." Judah is crowned the victor: "I crown their god." Pontius tells Ben-Hur: "I will send for you. I have a message from Rome. A long life Arrius, and the good sense to live it."

On his bloody death bed in a room beneath the coliseum, Messala has sent for Ben-Hur, delaying an operation to amputate his legs that will attempt to save his life. Messala hisses: "I don't receive him with half a body." Visited by Ben-Hur, the unrepentant Messala honors him:

Messala: Triumph complete, Judah. The race won. The enemy destroyed.
Ben-Hur: I see no enemy.
Messala: What do you think you see? The smashed body of a wretched animal! Is enough of a man still left here for you to hate? Let me help you...You think they're dead. Your mother and sister. Dead. And the race over. It isn't over, Judah. They're not dead.
Ben-Hur: Where are they? Where are they? (shouting) Where are they?
Messala: (vengefully) Look for them in the Valley of the Lepers, if you can recognize them. (grabbing Judah's clothing) It goes on. It goes on, Judah. The race, the race is not over.

He dies gloating at Judah's horror, exacting some revenge for his humiliating defeat by revealing that Ben-Hur's mother and sister have been condemned to live among lepers. Judah returns to the now-empty arena, stunned by the news.

Judah rushes to the hideous Valley of the Lepers on the outskirts of the city to search for his family members. He is warned to stay away by attendants dropping food to the outcasts with a pulley apparatus: "Are you a madman? Keep well out of this place." He discovers Esther with Malluch delivering food for Miriam and Tirzah.

Judah: (grabbing Esther) Why did you tell me they were dead?
Esther: It was what they wanted. Judah, you must not betray this faith. Will you do this for them?
Judah: Not to see them.

In his first view of them, the sight is so painful that he hides behind a boulder. He weeps when he hears Miriam ask Esther: "Is he happy?" Esther assures Miriam: "Yes, he is well. Your mind can be at rest for him. He is well, Miriam." Overcome, Judah cannot speak to them. When they have left, Esther advises him: "You can go back...They have one blessing left. To think you remember them as they were and live your own life. Forget what is here."

The film moves from the action of the previous scenes to sequences of religious mysticism. On his way back to Jerusalem, Ben-Hur and Esther meet Balthazar on the outskirts of a large crowd gathering to listen to a saintly preacher (called "the son of God") in the Sermon on the Mount. Ben-Hur doesn't realize this was the carpenter who brought him water at Nazareth many years earlier when he was a slave. With bitterness in his heart, Ben-Hur ignores the Sermon and goes on his own way, claiming he has "business with Rome." Balthazar realizes that he "insists on death."

Pontius Pilate has summoned Ben-Hur, to bring him a message from his father. The Emperor has made him a Roman citizen, but Ben-Hur can only associate Rome with cruelty:

Ben-Hur: I have just come from the Valley of Stone. My mother and sister live what's left of their lives. By Rome's will, lepers, outcasts without hope...Their flesh...carries Rome's mark...the deed was not Messala's. I knew him, well, before the cruelty of Rome spread in his blood. Rome destroyed Messala as surely as Rome has destroyed my family.
Pontius Pilate: Where there is greatness, great government or power, even great feeling or compassion, error also is great. We've progressed and matured by fault. But Rome has said she is ready to join your life to hers in a great future...not to crucify yourself on a shadow such as old resentment or impossible loyalties. Perfect freedom has no existence. The grown man knows the world he lives in, and for the present, the world is Rome.

Ben-Hur prefers to stay with his own people: "I am Judah Ben-Hur." The ruler re-asserts Roman authority:

Pontius Pilate: I become the hand of Caesar, ready to crush all those who challenge his authority. There are too many small men of envy and ambition who try to disrupt the government of Rome. You have become the victor and hero for these people. They look to you, their one true god as I called you. If you stay here, you will find yourself part of this tragedy.
Ben-Hur: I'm already part of this tragedy.

Judah returns his Roman seal-ring to Pontius for him to give back to Arrius. Pontius advises him one more time to leave Judea. When Judah returns home, Esther wishes that he rest and find peace - the message she had just heard in the sermon on the hill. But undeterred and consumed by rage and hatred, he asserts that his sole aim is "to wash this land clean" of Roman tyranny:

Esther: 'Blessed are the merciful, for they shall obtain mercy. Blessed are the peacemakers, for they shall be called the children of God.'
Judah (snapping back): Children of God! In that dead valley where we left them? I tell you, every man in Judea is unclean and will stay unclean until we've scoured off our bodies the crust and filth of being at the mercy of tyranny. No other life is possible except to wash this land clean.
Esther: In blood?
Judah: Yes, in blood.
Esther: I know there is a law in life. That blood begets more blood as dog begets dog. Death generates death. The vulture breeds the vulture. But the voice I heard on the hill today said, 'Love your enemy. Do good to those who despitefully use you.'
Judah: All who are born in this land hereafter can suffer as we have done.
Esther: As you make us do now! Are we to bear nothing together, even love?
Judah: I could hardly draw a breath without feeling you in my heart. Everything I do from this moment will be as great a pain to you as you have ever suffered. It is better not to love me!
Esther: It was Judah Ben-Hur I loved. What has become of him? You seem to be now the very thing you set out to destroy, giving evil for evil. Hatred is turning you to stone. It's as though you had become Messala! I've lost you Judah.

At the Valley of the Lepers, Esther tells Miriam that she is impressed by the preacher's words and miracles, and wishes Miriam and Tirzah to accompany her to see the new preacher in Jerusalem. Then, she learns from Miriam that this is not possible - Tirzah is dying. Ben-Hur rushes forward despite his mother's protests. He also hears that Tirzah is dying. Seeing Esther's faith in Jesus of Nazareth's message: "Life is everlasting. Death is nothing to fear if you have faith," Judah is persuaded to help take them to the great teacher.

In Jerusalem, they fortuitously arrive just in time to hear that 'the young rabbi' from Nazareth is on trial, now a political prisoner of the brutal Romans. Pontius Pilate condemns him and two other common criminals to death, washing his hands afterwards. Jesus is paraded through the streets - he struggles through the crowd, carrying a heavy cross on his back, ready to be crucified and put to death. Ben-Hur recognizes Jesus as the one who had previously given him a cup of water when he was on the slave galley march: "I know this man!" The moment of recognition occurs as the shadow of his cross passes over him as Jesus is on his way to Golgotha. Jesus stumbles in front of them. "In his pain, this look of peace," Miriam marvels.

Judah follows along behind, and as the carpenter once gave Ben-Hur water in Nazareth, so does Ben-Hur offer the agonized 'King of the Jews' water when he falls again. With hundreds of others, including Balthazar, Judah witnesses The King of the Jews being nailed to a cross and the agonizing crucifixion. Ben-Hur asks Balthazar: "What has he done to merit this?" Balthazar explains: "He has taken the world of our sins unto himself. To this end he said he was born, in that stable where I first saw him. For this cause, he came into the world." The wise Balthazar interprets it as a beginning, not a death.

In the grand and moving apocalyptic finale of the film, Miriam, Tirzah, and Esther are walking back to the Valley of the Lepers. Miriam and Tirzah have been transformed by their experience:

Miriam: As though he were carrying in that cross the pain of the world.
Tirzah: So fearful, and yet why is it? I'm not afraid any more.

They take shelter from an approaching thunderstorm in a cave. A strange darkness covers everything and a deafening rumbling is heard when Jesus' life ends. A howling wind roars, anticipating the fierce rainstorm. Blinding lightning and a bluish light illuminates their faces in the darkness, and their sores disappear. Ben-Hur's mother and dying sister are cured, healed of the disease of leprosy. Outside the cave, they let the healing waters of the rain strike their faces, purifying, renewing, and cleansing their lives. The blood from the cross, flowing from a supreme act of love, joins with the runoff from the rain and is gradually dispersed - a new beginning is signalled.

Ben-Hur is reunited with Esther back in their home. He describes the crucifixion experience to her, transfixed and transformed:

Almost at the moment he died, I heard him say it, 'Father, forgive them, for they know not what they do.'...Even then. And I felt His voice take the sword out of my hand.

In joy, he beholds his miraculously healed mother and sister. He understands that forgiveness, not blind vengeance, has changed him and the ultimate fate of his people.

The last image of the film is of the high place with three empty crosses. A shepherd drives his flock before the hill where the crucifixion took place.