Christian, an everyman character, is the protagonist of the allegory, which centres itself in his journey from his hometown, the "City of Destruction" ("this world"), to the "Celestial City" ("that which is to come": Heaven) atop Mount Zion. Christian is weighed down by a great burden—the knowledge of his sin—which he believed came from his reading "the book in his hand" (the Bible). This burden, which would cause him to sink into Hell, is so unbearable that Christian must seek deliverance. He meets Evangelist as he is walking out in the fields, who directs him to the "Wicket Gate" for deliverance. Since Christian cannot see the "Wicket Gate" in the distance, Evangelist directs him to go to a "shining light," which Christian thinks he sees. Christian leaves his home, his wife, and children to save himself: he cannot persuade them to accompany him. Obstinate and Pliable go after Christian to bring him back, but Christian refuses. Obstinate returns disgusted, but Pliable is persuaded to go with Christian, hoping to take advantage of the Paradise that Christian claims lies at the end of his journey. Pliable's journey with Christian is cut short when the two of them fall into the Slough of Despond, a boggy mire-like swamp where pilgrim's doubts, fears, temptations, lusts, shames, guilts, and sins of their present condition of being a sinner are used to sink them into the mud of the swamp. It is there in that bog where Pliable abandons Christian after getting himself out. After struggling to the other side of the slough, Christian is pulled out by Help, who has heard his cries and tells him the swamp is made out of the decadence, scum, and filth of sin, but the ground is good at the narrow Wicket Gate.
On his way to the Wicket Gate, Christian is diverted by the secular ethics of Mr. Worldly Wiseman into seeking deliverance from his burden through the Law, supposedly with the help of a Mr. Legality and his son Civility in the village of Morality, rather than through Christ, allegorically by way of the Wicket Gate. Evangelist meets the wayward Christian as he stops before Mount Sinai on the way to Mr. Legality's home. It hangs over the road and threatens to crush any who would pass it; also the mountain flashed with fire. Evangelist shows Christian that he had sinned by turning out of his way and tells him that Mr. Legality and his son Civility are descendants of slaves and Mr. Worldly Wiseman is a false guide, but he assures him that he will be welcomed at the Wicket Gate if he should turn around and go there, which Christian does.
At the Wicket Gate begins the "straight and narrow" King's Highway, and Christian is directed onto it by the gatekeeper Goodwill who saves him from Beelzebub's archers at Beelzebub's castle near the Wicket Gate and shows him the heavenly way he must go. In the Second Part, Goodwill is shown to be Jesus himself. To Christian's query about relief from his burden, Goodwill directs him forward to "the place of deliverance."
Christian makes his way from there to the House of the Interpreter, where he is shown pictures and tableaux that portray or dramatize aspects of the Christian faith and life. Roger Sharrock denotes them "emblems".
From the House of the Interpreter, Christian finally reaches the "place of deliverance" (allegorically, the cross of Calvary and the open sepulchre of Christ), where the "straps" that bound Christian's burden to him break, and it rolls away into the open sepulchre. This event happens relatively early in the narrative: the immediate need of Christian at the beginning of the story being quickly remedied. After Christian is relieved of his burden, he is greeted by three angels, who give him the greeting of peace, new garments, and a scroll as a passport into the Celestial City. Encouraged by all this, Christian happily continues his journey until he comes upon three men named Simple, Sloth, and Presumption. Christian tries to help them, but they disregard his advice. Before coming to the Hill of Difficulty, Christian meets two well-dressed men named Formality and Hypocrisy who prove to be false Christians that perish in the two, dangerous bypasses near the hill named Danger and Destruction. Christian falls asleep at the arbor above the hill and loses his scroll, forcing him to go back and get it. Near the top of the Hill of Difficulty, he meets two weak pilgrims named Mistrust and Timorous who tell him of the great lions of the Palace Beautiful. Christian frightfully avoids the lions through Watchful the porter who tells them that they are chained and put there to test the faith of pilgrims.
Atop the Hill of Difficulty, Christian makes his first stop for the night at the House of the Palace Beautiful, which is a place built by God for the refresh of pilgrims and godly travelers. Christian spends three days here, and leaves clothed with the Armor of God (Eph. 6:11–18), which stands him in good stead in his battle against the demonic dragon-like Apollyon, (the lord and god of the City of Destruction) in the Valley of Humiliation. This battle lasts "over half a day" until Christian manages to wound and stab Apollyon with his two-edged sword (a reference to the Bible, Heb. 4:12). "And with that Apollyon spread his dragon wings and sped away."
As night falls Christian enters the fearful Valley of the Shadow of Death. When he is in the middle of the Valley amidst the gloom, terror and demons, he hears the words of the Twenty-third Psalm, spoken possibly by his friend Faithful:
Yea, though I walk through the Valley of the Shadow of Death, I will fear no evil: for thou art with me; thy rod and thy staff they comfort me. (Psalm 23:4.)
As he leaves this valley the sun rises on a new day.
Just outside the Valley of the Shadow of Death he meets Faithful, also a former resident of the City of Destruction, who accompanies him to Vanity Fair, a place built by Beelzebub where every thing to a human's tastes, delights, and lusts are sold daily, where both are arrested and detained because of their disdain for the wares and business of the Fair. Faithful is put on trial, and executed by burning at the stake as a martyr. A celestial chariot then takes Faithful to the Celestial City, martyrdom being a shortcut there. Hopeful, a resident of Vanity Fair, takes Faithful's place to be Christian's companion for the rest of the way.
Christian and Hopeful then come to a mining hill called Lucre its owner named Demas offers them all the silver of the mine but Christian sees through Demas's trickery and they avoid the mine. Afterwards, a false pilgrim named By-Ends and his friends, who followed Christian and Hopeful only to take advantage of them, perish at the Hill Lucre, never to be seen or heard again. Along a rough, stony stretch of road, Christian and Hopeful leave the highway to travel on the easier By-Path Meadow, where a rainstorm forces them to spend the night. In the morning they are captured by Giant Despair, who is known for his savage cruelty and his wife Diffidence and takes them to his Doubting Castle, where they are imprisoned, beaten and starved. The Giant and the Giantess want them to commit suicide, but they endure the ordeal until Christian realizes that a key he has, called Promise, will open all the doors and gates of Doubting Castle. Using the key and the Giant's weakness to sunlight, they escape.
The Delectable Mountains form the next stage of Christian and Hopeful's journey, where the shepherds show them some of the wonders of the place also known as "Immanuel's Land". As at the Delectable Mountains, the pilgrims are shown sights that strengthen their faith and warn them against sinning like the Hill Error or the Mountain Caution. On Mount Clear they are able to see the Celestial City through the shepherd's "perspective glass", which serves as a telescope. This device is given to Mercy in the Second Part at her request. The shepherds tell the pilgrims to beware of the Flatterer and to avoid the Enchanted Ground. Soon they come to a crossroad and a man dressed in white comes to help them. Thinking he is a shining one, the pilgrims follow the man, but soon get stuck in a net and realize their so-called angelic guide was the Flatterer! A true shining one comes and frees them from the net. The Angel punishes them for following the Flatterer and then puts them back on the right path. The pilgrims meet Atheist, who tells them Heaven and God don't exist, but Christian and Hopeful remember the shepherds and pay no attention to the man. Christian and Hopeful come to a place where a man named Little-Faith is chained by the ropes of seven demons who take him to a shortcut to the Lake of Fire (Hell).
On the way, Christian and Hopeful meet a lad named Ignorance, who believes that he will be allowed into the Celestial City through his own good deeds rather than as a gift of God's grace. Christian and Hopeful meet up with him twice and try to persuade him to journey to the Celestial City in the right way. Ignorance persists in his own way that he thinks will lead him into Heaven. After getting over the River of Death on the ferry boat of Vain Hope without overcoming the hazards of wading across it, Ignorance appears before the gates of Celestial City without a passport, which he would have acquired had he gone into the King's Highway through the Wicket Gate. The Lord of the Celestial City orders the shining ones (angels) to take Ignorance to one of the byways of Hell and throw him in.
Christian and Hopeful make it through the dangerous Enchanted Ground (a place where the air makes them sleepy and they never wake up) into the Land of Beulah, where they ready themselves to cross the dreaded River of Death on foot to Mount Zion and the Celestial City. Christian has a rough time of it because of his past sins wearing him down, but Hopeful helps him over; and they are welcomed into the Celestial City.
The Second Part of The Pilgrim's Progress presents the pilgrimage of Christian's wife, Christiana; their sons; and the maiden, Mercy. They visit the same stopping places that Christian visited, with the addition of Gaius' Inn between the Valley of the Shadow of Death and Vanity Fair; but they take a longer time in order to accommodate marriage and childbirth for the four sons and their wives. The hero of the story is Great-Heart, a servant of the Interpreter, who is the pilgrims' guide to the Celestial City. He kills four giants called Giant Grim, Giant Maul, Giant Slay-Good, and Giant Despair and participates in the slaying of a monster called Legion that terrorizes the city of Vanity Fair.
The passage of years in this second pilgrimage better allegorizes the journey of the Christian life. By using heroines, Bunyan, in the Second Part, illustrates the idea that women as well as men can be brave pilgrims.
Alexander M. Witherspoon, professor of English at Yale University, writes in a prefatory essay:
Part II, which appeared in 1684, is much more than a mere sequel to or repetition of the earlier volume. It clarifies and reinforces and justifies the story of Part I. The beam of Bunyan's spotlight is broadened to include Christian's family and other men, women, and children; the incidents and accidents of everyday life are more numerous, the joys of the pilgrimage tend to outweigh the hardships; and to the faith and hope of Part I is added in abundant measure that greatest of virtues, charity. The two parts of The Pilgrim's Progress in reality constitute a whole, and the whole is, without doubt, the most influential religious book ever written in the English language.
This is exemplified by the frailness of the pilgrims of the Second Part in contrast to those of the First: women, children, and physically and mentally challenged individuals. When Christiana's party leaves Gaius's Inn and Mr. Feeble-Mind lingers in order to be left behind, he is encouraged to accompany the party by Greatheart:
But brother ... I have it in commission, to comfort the feeble-minded, and to support the weak. You must needs go along with us; we will wait for you, we will lend you our help, we will deny ourselves of some things, both opinionative and practical, for your sake; we will not enter into doubtful disputations before you, we will be made all things to you, rather than you shall be left behind.
The pilgrims learn of Madame Bubble who created the Enchanted Ground and Forgetful Green, a place in the Valley of Humiliation where the flowers make other pilgrims forget about God's love. Christiana, Matthew, Joseph, Samuel, James, Mercy, Great Heart, Mr. Feeble Mind, and Mr. Ready-To-Halt come to Bypath-Meadow and after much fight and difficulty; slay the cruel Giant Despair and the wicked Giantess Diffidence and demolish Doubting Castle for Christian and Hopeful who were oppressed there. They free a pale man named Mr. Despondency and his daughter named Much-Afraid from the castle's dungeons.
When the pilgrims end up in the Land of Beulah, they cross over the River of Death by appointment. As a matter of importance to Christians of Bunyan's persuasion reflected in the narrative of The Pilgrim's Progress, the last words of the pilgrims as they cross over the River of Death are recorded. The four sons of Christian and their families do not cross, but remain for the support of the church in that place.