While passing through the Valley of Humiliation, Christian is attacked by a devilish fiend named Apollyon, who nearly overpowers Christian with shameful reminders of what a sinner he is. Christian finally beats Apollyon using his sword, which is a metaphor for knowledge of the Bible:
Christian nimbly stretched out his hand for his Sword, and caught it, saying, Rejoice not against me, O mine Enemy! When I fall I shall arise; and with that gave him a deadly thrust, which made him give back, as one that had received his mortal wound: Christian, perceiving that, made at him again, saying, Nay, in all these things we are more than Conquerors through him that loved us. And with that Apollyon spread forth his Dragon's wings, and sped him away, that Christian for a season saw him no more.
Notice that each time Christian thrusts his sword at Apollyon, he quotes Scripture (the prophet Micah and the book of Romans, respectively). The sword, then, is a metaphor for the biblical truths that really do the devil harm. That's because the Bible teaches Christians that their allegiance is to God, not Satan, and that they conquer all their enemies, including Satan, through their faith in Christ. Bunyan's implication is that a Christian who knows and believes the Bible won't succumb to Satan's temptations or accusations in the end.
Note, though, that Apollyon flees just "for a season"—in other words, he'll be back, so Christian must keep his sword at the ready. In this way, Bunyan urges Christian readers to study their Bible and internalize its teachings, never letting their guard down.
When Christian and Hopeful meet the Shepherds in the Delectable Mountains, the Shepherds point out some would-be pilgrims in the distance who are stumbling around blindly. Blindness is used as a metaphor for losing one's way spiritually:
Then said the Shepherds, From that Stile there goes a path that leads directly to Doubting Castle, which is kept by Giant Despair; and these men (pointing to them among the Tombs) came once on Pilgrimage, as you do now [...] [The Giant Despair] at last did put out their eyes, and led them among those Tombs, where he has left them to wander to this very day, that the saying of the Wise Man might be fulfilled, He that wandereth out of the way of understanding, shall remain in the congregation of the dead. Then Christian and Hopeful looked upon one another, with tears gushing out[.]
The blind pilgrims have taken the same journey and faced some of the same obstacles as Christian and Hopeful—the latter have recently escaped from the Giant Despair in Doubting Castle, in fact—yet they evidently failed to overcome these obstacles. As a result, their situation is now the inverse of Christian and Hopeful's—instead of having their eyes fixed on their destination, they're unable to see it at all, and instead of progressing on their way, they wander helplessly among tombs. To drive this point home even further, the quote in italics, from Proverbs 21:16, implies that since the blind pilgrims can't discern the path ahead, they'll never attain eternal life but will remain among the doomed forever. The metaphor suggests that being blind and lost is the opposite of being on pilgrimage, which by its very nature is a focused and purposeful journey.
Witnessing this, Christian and Hopeful are far from triumphant; instead, they weep both for the blind pilgrims' fate and for the realization that the same thing almost happened to them, suggesting that there's a fine line between success and abject failure when one is on pilgrimage.
Earlier in the novel, Christiana's son Matthew had eaten fruit that belonged to the devil. Later, when the group is staying at the Porter's House, Matthew gets a terrible stomachache from the fruit, so, in Bunyan's metaphor for salvation from sin, an old doctor named Mr. Skill makes Matthew a:
[purge] to the purpose, ’twas made Ex Carne & Sanguine Christi. (You know Physicians give strange Medicines to their Patients.) And it was made up into Pills [...]. Now he was to take them three at a time fasting, in half a quarter of a pint of the Tears of Repentance.
There's a lot going on in this metaphor. First, ex Carne & Sanguine Christi is Latin for "from the body and blood of Christ." On a surface level, then, the purgative medicine could simply refer to Jesus Christ as the atoning sacrifice for Matthew's sin. On a more sophisticated level, it might be an allusion to the Christian sacrament of communion or the Eucharist, in which Christians believe that they partake of Christ's body and blood. Either or both references could be in play here, though given the narrator's aside about "strange Medicines," it's safe to assume that Bunyan is sticking to the more literal level. His greater point, after all, is that it's because of Christ's literal death that a sinner like Matthew (or any sinner) can be forgiven and "purged" of sin's effects.
In terms of Bunyan's Protestant theology, it's important to note that these special pills are only effective if taken with "Tears of Repentance," meaning that the pills won't work alone, but that the "patient" must be genuinely sorry for their sins in order for the healing effects of Christ's sacrifice to apply to them. The requirement to take the pills "fasting," or on an empty stomach, might be a further reference to the need for deep sorrow over sin, or it might also imply that the one who takes the pills shouldn't rely on any other remedy to heal them. The prescribed dose of three pills may be an allusion to the Holy Trinity, as is so often the case with symbolic "threes" in Christian literature.
Overall, the pills serve as a metaphor for the way a Christian is saved from sin—that is, by receiving Christ's sacrifice as one's only cure, something that can only be done with a repentant attitude. Though the metaphor appears in the context of a specific wrongdoing (Matthew eating the devil's fruit), it's meant to apply to any and all sins.
When Christiana's group of pilgrims passes through the Enchanted Ground, Bunyan uses a biblical allusion to show that faith is indispensable to their journey:
Now they had not gone far, but a great Mist and a Darkness fell upon them all, so that they could scarce for a great while see the one [or] the other. Wherefore they were forced for some time to feel for one another by Words, for they walked not by Sight.
"[T]hey walked not by Sight" is an allusion to 2 Corinthians 5:7, "For we walk by faith, not by sight." At this point in the New Testament letter, the apostle Paul exhorts Christians regarding the hope of eternal life. Even while Christians live life in their earthly bodies and are thus "absent from the Lord" in heaven, Paul explains in the preceding verse, they can be confident, knowing that someday they will enjoy eternal life with the Lord. They have this confidence "by faith" and not because they can see it with their eyes.
This allusion is a particularly apt one for Bunyan to insert while describing the group's journey through the Enchanted Ground, a place whose atmosphere tends to lull pilgrims asleep unless they make a concerted effort to stay alert. When Christiana's group passes through, the atmosphere is especially marked by a disorienting mist and darkness; they cannot rely on their sense of sight to find their way. Instead, the pilgrims keep talking in order to keep track of each other's locations as they go. By encouraging one another verbally, the pilgrims are able to ensure that nobody strays from the path and that everyone stays focused on their destination, even though they can't navigate by sight and be visibly assured that they're headed the right way. The struggle through the Enchanted Ground's mist and darkness also serves as a metaphor for the journey through earthly life, where the Christian hopes for eternal life with God even though that promise isn't accessible to the natural senses. As the Bible verse states, Christian confidence comes not from "sight," but from "faith"—and, Bunyan implies, faith in one's ultimate destination is maintained through mutual encouragement in a shared journey, not through wandering in solitude (a solitude that, implicitly, would tend to lead one astray).
