This is a story of religious persecution and the aftermath of displacement. During the Partition of India in 1947, Hindus and Sikhs were made to move to India, and Muslims were forced into Pakistan, regardless of family history. Some families were displaced after many generations of living in one place or the other.
As the refugees flee, they are exposed to constant violence which often crops up when Hindus and Muslims are in close proximity. Little by little, death and murder become the normal for these refugees. Muslims are deported on trains to Pakistan and Hindus on trains to India (nearly ten million in total) but within weeks, almost a million are already dead. The trains run continually, and people call them "ghost trains."
In this frenzy of chaos and violence is Mano Majra, one of the last remaining peaceful villages on the frontier. Mano Majra is diverse, made up of Hindus and Muslims, but also Sikhs and Christian sympathizers. They depend on each other and live in harmony. Train to Pakistan begins with the murder of Lala Ram Lal, the Mano Majra moneylender, and one of the few Hindus in the community.
A dacoit named Malli and his gang of robbers are the ones who kill Lala Ram Lal, but the inept police who oversee Mano Majra and the surrounding villages falsely imprison two men, Juggut “Jugga” Singh and Iqbal Singh, for the crime. The town badmash, Jugga is a large young man who has a bad reputation but a good heart. He is the lover of Nooran, the daughter of the village imam, and a bitter enemy of Malli. Iqbal Singh is a social worker from Delhi who comes to Mano Majra in hopes of inspiring the locals to take political action in the new India, but he instead gets caught up in the confusion and violence of the frontier.
The night of Lala Ram Lal’s murder, Jugga was having a tryst with Nooran, and Iqbal hadn’t yet arrived in Mano Majra. Still, the head constable arrests them, much to the chagrin of his superiors, the subinspector and the magistrate, Hukum Chand. A practical, if slightly corrupt man, Hukum Chand instructs the subinspector to keep Jugga and Iqbal in custody, but to continue looking for the true killers.
One day, a “ghost train” from Pakistan arrives in Mano Majra. The villagers don’t know the train is full of dead Hindus and Sikhs until the police and military burn the bodies. The outside world is finally pressing in, and no one knows what to do. The arrival of the ghost train leaves Hukum Chand shaken as well, and he must cling to Haseena, a young Muslim prostitute the subinspector arranged for him, in order to fall asleep. When he wakes up the next morning, the subinspector tells him Jugga gave him the names of the dacoits who killed Lala Ram Lal. The magistrate orders the arrest of Malli and his gang, but continues to keep Jugga and Iqbal imprisoned. He also tells the subinspector to contact the local Muslim refugee camp and arrange for the evacuation of the Mano Majra Muslims.
Malli and his gang are hauled in, but as a part of Hukum Chand’s plan to convince Mano Majra to evacuate its Muslim villagers, they are soon released. They are taken to the Sikh temple in the village, and stand by as the head constable implicates Iqbal and a group of Muslim dacoits in Lala Ram Lal’s murder. After sending these ripples through the town, the head constable finishes by announcing that all Muslims in Mano Majra will be taken to a local refugee camp.
These announcements, coupled with the arrival of the ghost train, split Mano Majra in half. Muslims and Sikhs begin to look at one another suspiciously. A group of Sikh Mano Majrans meet at the temple to discuss the recent events. One young man is infuriated and bitter towards his Muslim neighbors, until someone suggests that Sikh refugees from Pakistan may come to their village and harm their Muslims. The man’s loyalty to his neighbors overpowers his own religious biases, and he vows to defend his neighbors. Imam Baksh and two other Muslims join the group at the temple, and everyone discusses together what they should do. After they go back and forth, it’s decided that the Muslims will go to the camp for now. Imam Baksh leaves in tears to tell the other Muslims to pack up their property.
When her father tells her they must leave, Nooran runs to Jugga’s house, but he is still in jail. She talks to Jugga’s mother, and reveals that she’s pregnant with Jugga’s baby. Jugga’s mother calms her down, and convinces her that Jugga will find her wherever she is.
The next morning the convoy from the refugee camp arrives, but it can only take a limited amount of property. It’s also revealed that the Mano Majrans aren’t staying at the camp indefinitely, but will be deported to Pakistan. Panic ensues as everyone wonders what will happen to the Muslims’ property. The commanding officer doesn’t care, and gives the Muslims only 10 minutes to grab what they can carry and say their goodbyes. Malli is left in charge of the property, and once the convoy is out of sight his band of dacoits and the Sikh refugees from Pakistan raid and loot it.
Later that day, the Sutlej river begins to rise, and the focus of the village shifts to the dangers that presents. The lambardar arranges a night watch to monitor the river in case of flooding. As the men stand watch, they hear a train arrive at the Mano Majra train station. No one gets out. Meanwhile on the river, dead livestock, thatch, and clothing come floating down. When morning breaks, the men can clearly see the bodies of murdered men, women, and children bobbing in the water. It’s clear another massacre happened upstream. The men hurriedly return to the village to report the activity at the river, but find everyone’s eyes glued to the train station. The train that arrived is another ghost train, and this time the bodies are being disposed of in a mass grave.
At night, the atmosphere in Mano Majra is grim. All of the remaining villagers are gathered at the gurdwara, because none of them wants to be alone. After Meet Singh, the Sikh priest, ends his prayer, a group of militant Sikhs enter the temple. They intimidate some of the Mano Majrans into helping them massacre a train of Muslims headed to Pakistan. The train is coming from the refugee camp, which means Mano Majra’s Muslims will be on it. Despite their sorrow the day before, no one from Mano Majra besides Meet Singh and the lambardar speaks up and rejects the plan. Instead, several villagers, along with the Sikh refugees and Malli’s gang, join the plot.
The lambardar goes to the police station at Chundunnugger and tells the subinspector of the planned attack. Hukum Chand is flippant and tells the subinspector to let the Sikhs kill the Muslims as long as the police aren’t implicated, until the subinspector tells him that Haseena will also be on the train. At this news, Hukum Chand completely switches his position, and comes up with a plan to save the train. He orders the release of Jugga and Iqbal, hoping that they will somehow save the Muslims on the train. As the subinspector releases the two men, he tells them the Mano Majra Muslims were evacuated, and that things in the village are very different.
When Jugga and Iqbal reach Mano Majra, Jugga disappears to look for Nooran, hoping that she has waited for him in the woods. Iqbal returns to the gurdwara, where Meet Singh greets him and tells him of the planned attack. Iqbal is appalled, but ultimately decides to do nothing, because no one would know of his sacrifice. He falls asleep drinking whisky, as Jugga comes to the temple seeking a prayer. Meet Singh reluctantly agrees to pray over him, but doesn’t explain what the prayer means when Jugga asks. Jugga thanks the priest anyways, and asks him to say goodbye to Iqbal for him.
At the rest house, Hukum Chand remembers people he knows who suffered because of the partition, and wishes that Haseena had stayed with him instead of going to her town. As the train approaches Mano Majra, he begins to cry and pray. At the bridge, the mob is in place. As they hear the train and watch it approach, they don’t notice a big man climbing the bridge until he reaches the top. The man pulls out a knife and begins to hack at the rope intended to kill the Muslims sitting on top of the train. The mob begins to shoot the man, but he persists. Just as the train reaches the bridge, the bullets cause the man to fall, but the rope breaks with him. The train rolls over him and continues, unscathed, on the way to Pakistan.