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From my bestselling 1996 book, A Biblical Defense of Catholicism, pp. 123-145. The introductory material of the chapter (definitions) is omitted; also a few quotations. Footnoting numbers are from my original manuscript and differ from the present Sophia edition. All Bible passages are from RSV.
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Psalm 66:12 Thou didst let men ride over our heads; we went through fire and through water; yet thou hast brought us forth to a spacious place.
This verse was considered a proof of purgatory by Origen  and St. Ambrose,  who posits the water of baptism and the fire of purgatory.
Ecclesiastes 12:14 For God will bring every deed into judgment, with every secret thing, whether good or evil.
Isaiah 4:4 When the Lord shall have washed away the filth of the daughters of Zion and cleansed the bloodstains of Jerusalem from its midst by a spirit of judgment and by a spirit of burning. (see also Isaiah 1:25-26)
St. Francis de Sales, the great Catholic apologist of the 16th century, commented on this verse as follows:
This purgation made in the spirit of judgment and of burning is understood of Purgatory by St. Augustine, in the 20th Book of the City of God, chapter 25. And in fact this interpretation is favoured by the words preceding, in which mention is made of the salvation of men, and also by the end of the chapter, where the repose of the blessed is spoken of; wherefore that which is said — “the Lord shall wash away the filth” — is to be understood of the purgation necessary for this salvation. And since it is said that this purgation is to be made in the spirit of heat and of burning, it cannot well be understood save of Purgatory and its fire. .
Isaiah 6:5-7 And I said:”Woe is me! for I am lost; for I am a man of unclean lips, and I dwell in the midst of a people of unclean lips; for my eyes have seen the King, the Lord of hosts.” Then flew one of the seraphim to me, having in his hand a burning coal which he had taken with tongs from the altar. And he touched my mouth, and said: “Behold, this has touched your lips; your guilt is taken away, and your sin forgiven.“
This passage is a noteworthy example of what happens when men experience God’s presence directly. An immediate recognition of one’s own unholiness occurs, along with the corresponding feeling of inadequacy. Like Isaiah, we must all undergo a self-conscious and voluntary purging upon approaching God more closely than in this present life.
Few doctrines are clearer in Scripture than the necessity of absolute holiness in order to enter heaven. On this, Protestants and Catholics are in total agreement. Therefore, the fundamental disagreement on this subject is: how long does this purification upon death take? Certainly, it cannot be logically denied as a possibility that this purging might involve duration.
4 Homily 25 on Numbers.
5 In Ps. 36; Sermon 3 on Ps. 118.
6 St. Francis de Sales, The Catholic Controversy (CON), tr. Henry B. Mackey, Rockford, IL: TAN Books, 1989 (orig. 1596), 358 (Part 3, Article 2: “Purgatory”).
Micah 7:8-9 Rejoice not over me, O mine enemy; when I fall, I shall rise; when I sit in darkness, the Lord will be a light to me. I will bear the indignation of the Lord because I have sinned against him, until he pleads my cause and executes judgment for me. He will bring me forth to the light; I shall behold his deliverance. (see also Leviticus 26:41,43, Job 40:4-5, Lamentations 3:39)
St. Jerome (d.420) considered this a clear proof of purgatory. 
Malachi 3:2-4 But who can endure the day of his coming, and who can stand when he appears? For he is like a refiner’s fire, and like fullers’ soap; he will sit as a refiner and purifier of silver, and he will purify the sons of Levi, and refine them like gold and silver, till they present right offerings to the Lord. Then the offering of Judah and Jerusalem will be pleasing to the Lord as in the days of old and as in former years.
7 Ibid., 358.
St. Francis de Sales recounts the patristic views on this passage:
This place is expounded of a purifying punishment by Origen (Hom. 6 on Exodus), St. Ambrose (On Ps 36), St. Augustine (City of God, Bk. 20, ch. 25), and St. Jerome (on this place). We are quite aware that they understand it of a purgation which will be at the end of the world by the general fire and conflagration, in which will be purged away the remains of the sins of those who will be found alive; but we still are able to draw from this a good argument for our Purgatory. For if persons at that time have need of purgation before receiving the effects of the benediction of the supreme Judge, why shall not those also have need of it who die before that time, since some of these may be found at death to have remains of their imperfections . . . St. Irenaeus in this connection, in chapter 29 of Book V, says that because the militant Church is then to mount up to the heavenly palace of the Spouse, and will no longer have time for purgation, her faults and stains will there and then be purged away by this fire which will precede the judgment. 
2 Maccabees 12:39-42, 44-45 . . . Judas and his men went to take up the bodies of the fallen . . . Then under the tunic of every one of the dead they found sacred tokens of the idols of Jamnia, which the law forbids the Jews to wear . . . So they all . . . turned to prayer, beseeching that the sin which had been committed might be wholly blotted out . . . For if he were not expecting that those who had fallen would rise again, it would have been superfluous and foolish to pray for the dead. But if he was looking to the splendid reward that is laid up for those who fall asleep in godliness, it was a holy and pious thought. Therefore he made atonement for the dead, that they might be delivered from their sin.
The Jews offered atonement and prayer for their deceased brethren, who had clearly violated Mosaic Law. Such a practice presupposes purgatory, since those in heaven wouldn’t need any help, and those in hell are beyond it. The Jewish people, therefore, believed in prayer for the dead (whether or not this book is scriptural — Protestants deny that it is). Jesus Christ did not correct this belief, as He surely would have done if it were erroneous (see Matthew 5:22,25-26, 12:32, Luke 12:58-59, 16:9,19-31 below). When our Lord and Savior talks about the afterlife, He never denies the fact that there is a third state, and the overall evidence of His utterances in this regard strongly indicates that He accepted the existence of purgatory.
Matthew 5:22 But I say to you that every one who is angry with his brother shall be liable to judgment; whoever insults his brother shall be liable to the council, and whoever says, “You fool!” shall be liable to the hell of fire.
St. Francis de Sales elucidates the implications of this statement of Christ:
It is only the third sort of offence which is punished with hell; therefore in the judgment of God after this life there are other pains which are not eternal or infernal, — these are the pains of Purgatory. One may say that the pains will be suffered in this world; but St. Augustine and the other Fathers understand them for the other world. And again may it not be that a man should die on the first or second offence which is spoken here? And when will such a one pay the penalty due to his offence? . . . Do then as the ancient Fathers did, and say that there is a place where they will be purified, and then they will go to heaven above. 
9 St. Francis de Sales, CON, 359-360.
10 Ibid., 373-374.
Matthew 5:25-26 Make friends quickly with your accuser, while you are going with him to court, lest your accuser hand you over to the judge, and the judge to the guard, and you be put in prison; truly, I say to you, you will never get out till you have paid the last penny. (see also Luke 12:58-59)
St. Francis de Sales:
Origen, St. Cyprian, St. Hilary, St. Ambrose, St. Jerome, and St. Augustine say that the way which is meant in the whilst thou art in the way [while you are going with him to court] is no other than the passage of the present life: the adversary [accuser] will be our own conscience, . . . as St. Ambrose expounds, and Bede, St. Augustine, St. Gregory [the Great], and St. Bernard. Lastly, the judge is without doubt Our Lord . . . The prison, again, is . . . the place of punishment in the other world, in which, as in a large jail, there are many buildings; one for those who are damned, which is as it were for criminals, the other for those in Purgatory, which is as it were for debt. The farthing, [penny] . . . are little sins and infirmities, as the farthing is the smallest money one can owe.
Now let us consider a little where this repayment . . . is to be made. And we find from most ancient Fathers that it is in Purgatory: Tertullian,  Cyprian,  Origen,  . . . St. Ambrose,  St. Jerome  . . . Who sees not that in St. Luke the comparison is drawn, not from a murderer or some criminal, who can have no hope of escape, but from a debtor who is thrown into prison till payment, and when this is made is at once let out? This then is the meaning of Our Lord, that whilst we are in this world we should try by penitence and its fruits to pay, according to the power which we have by the blood of the Redeemer, the penalty to which our sins have subjected us; since if we wait till death we shall not have such good terms in Purgatory, when we shall be treated with severity of justice. 
Matthew 12:32 And whoever says a word against the Son of man will be forgiven; but whoever speaks against the Holy Spirit will not be forgiven, either in this age or in the age to come.
If sins can be pardoned in the “age to come” (the afterlife), again, in the nature of things, this must be in purgatory. We would laugh at a man who said that he would not marry in this world or the next (as if he could in the next — see Mark 12:25). If this sin cannot be forgiven after death, it follows that there are others which can be. Accordingly, this interpretation was held by St. Augustine,  St. Gregory the Great,  Bede,  and St. Bernard,  among others.
11 The Soul, 100,10.
12 Epistle 4,2.
13 Homily 35 on Luke 12.
14 Commentary on Luke 12.
15 Commentary on Matthew 5.
16 St. Francis de Sales,CON, 372-373.
17 City of God, 21:24.
18 Dialogues, 4,39.
19 Commentary on Mark 3.
20 Homily 66 in Cant.
Luke 16:9 And I tell you, make friends for yourselves by means of unrighteous mammon, so that when it fails they may receive you into the eternal habitations. (read Luke 16:1-13 for the context)
St. Francis de Sales:
To fail, — what is it but to die? — and the friends, — who are they but the Saints? The interpreters all understand it so; whence two things follow, — that the Saints can help men departed, and that the departed can be helped by the Saints . . . Thus is this passage expounded by St. Ambrose, and by St. Augustine.  But the parable Our Lord is using is too clear to allow us any doubt of this interpretation; for the similitude is taken from a steward who, being dismissed from his office and reduced to poverty [16:2], begged help from his friends, and Our Lord likens the dismissal unto death, and the help begged from friends unto the help one receives after death from those to whom one has given alms. This help cannot be received by those who are in Paradise or in hell; it is then by those who are in Purgatory. 
Luke 16:19-31 There was a rich man who was clothed in purple and fine linen and who feasted sumptuously every day. And at his gate lay a poor man named Lazarus, full of sores, who desired to be fed with what fell from the rich man’s table; . . . the poor man died and was carried by the angels to Abraham’s bosom. The rich man also died and was buried; and in Hades, being in torment, he lifted up his eyes, and saw Abraham far off and Lazarus in his bosom. And he called out, “Father Abraham, have mercy upon me, and send Lazarus to dip the end of his finger in water and cool my tongue; for I am in anguish in this flame.” But Abraham said, “Son, remember that you in your lifetime received your good things, and Lazarus in like manner evil things, but now he is comforted here, and you are in anguish. And besides all this, between us and you a great chasm has been fixed, in order that those who would pass from here to you may not be able, and none may cross from there to us.” And he said, “Then I beg you, father, to send him to my father’s house, for I have five brothers, so that he may warn them, lest they also come into this place of torment.” But Abraham said, “They have Moses and the prophets; let them hear them.” And he said, “No, father Abraham; but if some one goes to them from the dead, they will repent.” He said to him, “If they do not hear Moses and the prophets, neither will they be convinced if some one should rise from the dead.”
Zechariah 9:11 As for you also, because of the blood of my covenant with you, I will set your captives free from the waterless pit.
Ephesians 4:8-10. . . “When he ascended on high he led a host of captives, and he gave gifts to men.” (In saying, “he ascended,” what does it mean but that he had also descended into the lower parts of the earth? He who descended is he who also ascended far above all the heavens, that he might fill all things.)
1 Peter 3:19-20 . . . he went and preached to the spirits in prison, who formerly did not obey, when God’s patience waited in the days of Noah, during the building of the ark, in which a few, that is, eight persons, were saved through water. (see also 4:6)
21 City of God, 12:27.
22 St. Francis de Sales, CON, 374-375.
Catholic commentator George Leo Haydock states:
Abraham’s bosom — The place of rest, where the souls of the saints resided, till Christ had opened heaven by his death . . . The bosom of Abraham (the common Father of all the faithful) was the place where the souls of the saints, and departed patriarchs, waited the arrival of their Deliverer. It was thither that Jesus went after his death; as it is said in the Creed, he descended into hell, to deliver those who were detained there, and who might at Christ’s ascension enter into heaven (see 1 Peter 3:19, Matthew 8:11) . . .
[on 1 Peter 3:19-20]: These spirits in prison, to whom Christ went to preach after his death, were not in heaven, nor yet in the hell of the damned; because heaven is no prison, and Christ did not go to preach to the damned . . . In this prison souls would not be detained unless they were indebted to divine justice, nor would salvation be preached to them unless they were in a state that was capable of receiving salvation. 
At the very least, these passages prove that there can and does exist a third (and intermediate) state after death besides heaven and hell. Thus, purgatory is not a priori unthinkable from a biblical perspective (as many Protestants casually assume). True, the Hebrew Sheol (Greek Hades — netherworld) is not absolutely identical to purgatory (both righteous and unrighteous go there), but it is nevertheless strikingly similar. Sheol is referred to frequently throughout the Old Testament (Deuteronomy 32:22, 2 Samuel 22:6, Psalm 16:10, 18:5, 55:15, 86:13, 116:3, 139:8, Proverbs 9:18, 23:14, Isaiah 5:14, 14:9,15, Ezekiel 31:16-17, 32:21,27). In Jewish apocalyptic literature (in the few hundred years before Christ), the notion of divisions in Sheol is found (for instance, in Enoch 22:1-14).
The Christian hell is equivalent to the New Testament Gehenna or “Lake of Fire”. Gehenna was literally the burning ash-heap outside Jerusalem, and was used as the name for hell by Christ (Matthew 5:22,29-30, 10:28, 18:9, 23:15,33, Mark 9:43,45,47, Luke 12:5 — cf. James 3:6). “Lake of fire” occurs only in Revelation as a chilling description of the horrors of hell into which the damned would be thrown (Revelation 19:20, 20:10,14-15, 21:8).
We know from Scripture that a few Old Testament saints went to heaven before Christ went to Sheol and led (presumably) the majority of the pre-Christian righteous there (Ephesians 4:8-10 and 1 Peter 3:19-20). Elijah went straight to heaven by a whirlwind, as we are informed in 2 Kings 2:11. It is also generally thought by all sides that Enoch went directly to heaven as well (Genesis 5:24). Moses came with Elijah to the Mount of Transfiguration to talk with Jesus (Matthew 17:1-3, Mark 9:4, Luke 9:30-31). By implication, then, it could be held that he, too, had been in heaven, and by further logical inference, other Old Testament saintly figures.
It follows that, even before Christ, there was a “two-tiered” afterlife for the righteous: some, such as Elijah, Enoch and likely Moses and others, went to heaven, whereas a second, larger group went temporarily to Sheol. Likewise, now the elect of God can go straight to heaven if sufficiently holy, or to purgatory as a necessary stopping-point in order to attain to the proper sanctity becoming of inhabitants of heavenly glory. Therefore, it is neither true that all righteous dead before Christ went solely to Sheol, nor that all after His Resurrection went, and go, to heaven. On the other hand, the reprobate dead in Sheol (or Hades) eventually are sentenced to hell (Revelation 20:13-15).
John Henry Cardinal Newman comments:
Our Saviour, as we suppose, did not go to the abyss assigned to the fallen Angels, but to those mysterious mansions where the souls of all men await the judgment. That He went to the abode of blessed spirits is evident, from His words addressed to the robber on the cross, when He also called it Paradise; that He went to some other place besides Paradise may be conjectured from St. Peter’s saying, He went and preached to the spirits in prison, who had once been disobedient (1 Peter 3:19-20). The circumstances then that these two abodes of disembodied good and bad, are called by one name, Hades, . . . seems clearly to show that Paradise is not the same as Heaven, but a resting-place at the foot of it. Let it be further remarked, that Samuel, when brought from the dead, in the witch’s cavern, said Why hast thou disquieted me, to bring me up? (1 Samuel 28:15), words which would seem quite inconsistent with his being then already in Heaven. 
1 Corinthians 3:11-15 For no other foundation can anyone lay than that which is laid, which is Jesus Christ. Now if any one builds on the foundation with gold, silver, precious stones, wood, hay, stubble – each man’s work will become manifest; for the Day will disclose it, because it will be revealed with fire, and the fire will test what sort of work each one has done. If the work which any man has built on the foundation survives, he will receive a reward. If any man’s work is burned up, he will suffer loss, though he himself will be saved, but only as through fire.
This is a clear and obvious allusion to purgatory, or at least, even for the most skeptical person, something exceedingly similar to it. Thus thought the Fathers, such as St. Cyprian,  St. Ambrose, St. Jerome,  St. Gregory the Great,  Origen,  and St. Augustine:
Lord, rebuke me not in Your indignation, nor correct me in Your anger [Psalm 38:1]. . . . In this life may You cleanse me and make me such that I have no need of the corrective fire, which is for those who are saved, but as if by fire . . . For it is said: He shall be saved, but as if by fire [1 Corinthians 3:15]. And because it is said that he shall be saved, little is thought of that fire. Yet plainly, though we be saved by fire, that fire will be more severe than anything a man can suffer in this life. 
St. Francis de Sales observes:
The Apostle uses two similitudes. The first is of an architect who with solid materials builds a valuable house on a rock: the second is of one who on the same foundation erects a house of boards, reeds, straw. Let us now imagine that a fire breaks out in both the houses. That which is of solid material will be out of danger, and the other will be burnt to ashes. And if the architect be in the first he will be whole and safe; if he be in the second, he must, if he would escape, rush through fire and flame, and shall be saved yet so that he will bear the marks of having been in fire . . . The fire by which the architect is saved can only be understood of the fire of Purgatory . . . . . .
When he . . . speaks of him who has built on the foundation, wood, straw, stubble, he shows that he is not speaking of the fire which will precede the day of judgment, since by this will pass not only those who have built with these light materials, but also those who shall have built in gold, silver, etc. All this interpretation, besides that it agrees very well with the text, is also most authentic, as having been followed with common consent by the ancient Fathers. 
1 Corinthians 15:29 Otherwise, what do people mean by being baptized on behalf of the dead? If the dead are not raised at all, why are people baptized on their behalf?
St. Francis de Sales:
This passage properly understood evidently shows that it was the custom of the primitive Church to watch, pray, fast, for the souls of the departed. For, firstly, in the Scriptures to be baptized is often taken for afflictions and penances; as in Luke 12:50 . . . and in St. Mark 10:38-9 . . . — in which places Our Lord calls pains and afflictions baptism [cf. Matthew 3:11, 20:22-3, Luke 3:16].
This then is the sense of that Scripture: if the dead rise not again, what is the use of mortifying and afflicting oneself, of praying and fasting for the dead? And indeed this sentence of St. Paul resembles that of 2 Maccabees 12:44 [cited above]: It is superfluous and vain to pray for the dead if the dead rise not again. . . . Now it was not for those in Paradise [heaven], who had no need of it, nor for those in hell, who could get no benefit from it; it was, then, for those in Purgatory. Thus did St. Ephraim [d.373] expound it. 
The “penance” interpretation is supported contextually by the next three verses, where the Apostle speaks of being in peril every hour, and dying every day. St. Paul certainly doesn’t condemn the practice, whatever it is (his question being merely rhetorical). Given these facts, and the striking resemblance to 2 Maccabees 12:44, the traditional Catholic interpretation seems the most plausible.
In any event, Protestants are at almost a complete loss in coherently explaining this verse — one of the most difficult in the New Testament for them to interpret. It simply does not comport with their theology, which utterly disallows any penitential or prayerful efforts on behalf of the deceased.
2 Corinthians 5:10 For we must all appear before the judgment seat of Christ, so that each one may receive good or evil, according to what he has done in the body.
Our sins are judged here rather than forgiven, and this takes place in the next life. The standard Protestant theology of the judgment seat of Christ is not dissimilar to the notion of the chastising purifications of purgatory. There is a direct relation between judgment and the purging of sin. We are punished, in some fashion — or so St. Paul tells us in this verse — for evil deeds done. The pains of purgatory are roughly identical, or else highly akin, to this punishment, since they are the taking away of those sinful habits, tendencies, and affinities to which we have become attached. Conversely, we are rewarded for good deeds. As there are differential rewards for righteousness, so there are differential sufferings in purgatory for unrighteousness, so that a certain parallelism exists between the two concepts.
This passage is a sort of liaison between the theological categories justification and purgatory (and penance) — the former being the “positive” establishment of sanctity, and the latter being the “negative” removal of unholiness. This congruity between reward and punishment is even more clearly seen in 1 Corinthians 3:11-15 above, where St. Paul freely intermingles rewards and punishments, in the context of purgatorial fire. Given the obvious affinity of that passage with this one, each can be legitimately interpreted in light of the other. In doing so, the Catholic interpretation, with its distinctive understanding of faith and works, penance and purgatory, is more satisfactory exegetically than the usual Protestant interpretations, which are uncomfortable, by and large, with differential rewards and punishments (seeing these as somewhat incompatible with faith alone).
2 Corinthians 7:1. . . let us cleanse ourselves from every defilement of body and spirit, and make holiness perfect in the fear of God.(see also 1 Thessalonians 3:13, 4:7)
Here is a description of that analogous process of sanctification in this life which will be greatly intensified and made completely efficacious in the next, in purgatory.
Philippians 2:10-11 That at the name of Jesus every knee should bow, in heaven and on earth and under the earth, and every tongue confess that Jesus Christ is Lord, to the glory of God the Father.
Revelation 5:3,13 And no one in heaven or on earth or under the earth was able to open the scroll or to look into it. . . .And I heard every creature in heaven and on earth and under the earth and in the sea, and all therein, saying, “To him who sits upon the throne and to the Lamb be blessing and honour and glory and might for ever and ever!”
If God refuses to receive prayer, praise and worship from the unrepentant sinner (Psalm 66:18, Proverbs 1:28-30, Isaiah 1:15, 59:2, Jeremiah 6:20, Amos 5:21-24, Micah 3:4, Malachi 1:10, John 9:31, Hebrews 10:38), why would He permit the damned to undertake this practice?
Furthermore, if God does not compel human beings to follow Him and to enjoy His presence for eternity contrary to their free will, then it seems that He would not — as far as we can tell from Scripture — compel them to praise Him, as this would be meaningless, if not repulsive.
Therefore, “under the earth” must refer to purgatory. Revelation 5:13 especially makes sense under this interpretation, as the praise spoken there does not in any way appear forced, but rather, heartfelt and seemingly spontaneous (which would not be at all expected of persons eternally consigned to hell — see Matthew 8:29, Luke 4:34, 8:28, James 2:19).
Some Protestant commentators readily admit that “under the earth” is a reference to those in Sheol or Hades. Granting this interpretation for the sake of argument, most Protestants would presumably regard Hades in this instance (after Christ’s death — see Revelation 5:12) as simply the “holding tank” for those ultimately destined for hell (the elect having been taken to heaven by Christ). But this leads straight back to the exegetical problem of God neither desiring nor accepting such praise from even the obstinate sinner, let alone the damned.
The acceptance of a third, intermediate state in the afterlife for the righteous as well as the reprobate, even after Christ’s Resurrection, is a seriously troublesome position if one holds to the tenets of mainstream Reformational eschatological theology. For — given the Protestant view on justification — why would (or should) there be any second state for the “saved” once the road to heaven was paved by Christ? This state of affairs leads inexorably to considerations of differential merit and reward, such that a whole class is relegated to continued separation from Christ in some partial sense, and by implication, punishment, since these children of God have not yet attained to full union with God in eternal happiness and bliss.
Once it is conceded that (dead) righteous men praise God from “under the earth,”the standard Protestant position of all the saved “going straight to heaven at death” crumbles, for the simple reason that this group is contrasted with those in heaven. Furthermore, a position that “under the earth” refers metaphorically to merely all dead righteous (who, according to Protestantism are in heaven), makes the phraseology of Philippians 2:10 and Revelation 5:3,13 absurdly redundant, since St. Paul and St. John would be saying, “Those in heaven, and on earth, and in heaven . . . .”
Again, the only reasonable alternate interpretation, given all the above data, is to posit the existence of purgatory, from which praise to God emanates — it being that portion of the Church stationed for a time in the portico of heaven, so to speak.
2 Timothy 1:16-18 May the Lord grant mercy to the household of Onesiphorus, for he often refreshed me; he was not ashamed of my chains,but when he arrived in Rome he searched for me eagerly and found me — may the Lord grant him to find mercy from the Lord on that Day — and you well know all the service he rendered at Ephesus.
Onesiphorus appears to be dead at the time St. Paul writes this letter to Timothy. If that is true, then Paul is praying for the dead. One well-known Protestant commentary  admits that Onesiphorus is likely dead, citing the cross-reference of 2 Timothy 4:19, yet takes the remarkably incoherent position that St. Paul is praying for his conduct in life and reward at the Judgment. Thus, the admitted prayer (1:18), since it supposedly refers to the earthly life of the intended recipient, somehow thereby ceases to be a prayer for the dead even though it is pleading for mercy on the Day of Judgment for one who has indeed departed!
Now, of course, St. Paul could also pray for a living person to be recompensed justly by God, but this is missing the point, and is an example of the classic logical fallacy of proposing a “distinction without a difference.” For what distinguishes prayers for a living or a dead man, where the final Judgment is concerned?
Protestants say that it is impermissible to pray for the dead on this score since their fate is already sealed and it will be to no avail. The error here lies in the fact that the person’s fate had always been known (God being omniscient and out of time, foreordaining in a mysterious way the beginning and end of all things). In both cases our knowledge is paltry and altogether insufficient as to the person’s destiny. We pray out of charity (or, “desire,” as it were), and because we are commanded to, having been assured by the inspired biblical revelation that it has an effect.
The Jamieson, Fausset and Brown Commentary, another respected evangelical reference, takes a different position: “His household would hardly retain his name after the master was dead . . . Nowhere has Paul prayers for the dead, which is fatal to the theory . . . that he was dead.” 
But Word Pictures in the New Testament, a six-volume linguistic commentary by the great Greek scholar A.T. Robertson, states: “Apparently Onesiphorus is now dead as is implied by the wish in 1:18.” 
On the face of it, why couldn’t St. Paul be referring to the house of Onesiphorus in the same sense in which we speak of a deceased person’s “surviving wife and children?” His statement in 1:18 is similar to our spontaneous utterances at funerals, such as “May God rest his soul,” etc. (sometimes spoken or thought despite theologies to the contrary). And if Paul is “wishing” for benefits for the soul of a dead man, as Robertson holds, how is this essentially any different from praying for the dead?
To conclude, of the three prominent evangelical Protestant commentaries surveyed, two hold that St. Paul is “praying,” and one that he is “wishing.” Two conclude that Onesiphorus is probably dead, with a third denying this. It might be supposed with good reason that if reputable, scholarly Protestant commentators are more or less forced into (for them) uncomfortable positions due to the inescapable clarity of a text, perhaps the Catholic interpretation is the best one, as it requires no unnatural straining. All that is necessary is the willingness to accept the practice of prayers for the dead, for which there is ample scriptural warrant, Jewish precedent, and abundant support in the early Christian Church, as will be demonstrated subsequently.
Hebrews 12:14 Strive for peace with all men, and for the holiness without which no one will see the Lord. (see also 12:1,5-11,15,23, Ephesians 5:5, 1 Thessalonians 4:3 1 John 3:2-3)
John Henry Cardinal Newman writes:
The truth itself is declared in one form or another in every part of Scripture. It is told us again and again, that to make sinful creatures holy was the great end which our Lord had in view in taking upon Him our nature, and thus none but the holy will be accepted for His sake at the last day. The whole history of redemption, the covenant of mercy in all its parts and provisions, attests the necessity of holiness in order to salvation; as indeed even our natural conscience bears witness also . . .
Even supposing a man of unholy life were suffered to enter heaven, he would not be happy there; so that it would be no mercy to permit him to enter . . . We conclude that any man, whatever his habits, tastes, or manner of life, if once admitted into heaven, would be happy there . . . [But] here every man can do his own pleasure, but there he must do God’s pleasure . . . . . Let us alone! What have we to do with thee? is the sole thought and desire of unclean souls, even while they acknowledge His majesty. None but the holy can look upon the Holy One; without holiness no man can endure to see the Lord . . .
Heaven is not heaven, is not a place of happiness except to the holy . . . There is a moral malady which disorders the inward sight and taste; and no man labouring under it is in a condition to enjoy what Scripture calls the fulness of joy in God’s presence, and pleasures at His right hand forevermore. 
Newman explains (in effect) why purgatory (which he accepts elsewhere, even before his conversion to Catholicism in 1845) is a necessary and indeed, ultimately desirable process for all of us imperfect sinners to undergo, in order to properly approach God in His unfathomable majesty and holiness.
Hebrews 12:29 . . . our God is a consuming fire.
(see also Exodus 3:2-6, 19:18, 24:17, Numbers 31:23, Deuteronomy 4:24, 9:3, Psalm 66:10-12, Malachi 3:2, 4:1, Hebrews 10:27, 31)
Revelation 21:27 But nothing unclean shall enter it, nor any one who practises abomination or falsehood, but only those who are written in the Lamb’s book of life.
The relevance of this biblical data in terms of its analogy to the idea of purgatory is clear. The abundance of such scriptural evidence for purgatory led to a consensus among the Church Fathers as well. Protestant church historian Philip Schaff, who can definitely be considered a “hostile witness” as pertains this topic, summarized the belief of the early Christian Church:
These views of the middle state in connection with prayers for the dead show a strong tendency to the Roman Catholic doctrine of Purgatory . . . there are traces of the purgatorial idea of suffering the temporal consequences of sin, and a painful struggle after holiness . . . The common people and most of the fathers understood it of a material fire; but this is not a matter of faith . . . A material fire would be very harmless without a material body. 
Despite all this, Protestantism rejected the beliefs in purgatory and prayers for the dead, with the exception of Anglicans, many of whom have retained some form of these. Popular Christian apologist C. S. Lewis was one of these traditional Anglicans. In one of his last books, Letters to Malcolm: Chiefly on Prayer,  he stated that he prayed for the dead, among whom were many of his loved ones, and that he believed in purgatory, comparing it to an intense rinsing of the mouth at the dentist’s office. He thought no one would want to enter heaven unclean, as this would be downright embarrassing.
23 Haydock’s Catholic Family Bible and Commentary, New York: 1859; rep. Monrovia, CA: Catholic Treasures, 1991, 1376-1377, 1611.
24 Sermon: “The Intermediate State,” 1836.
25 Book 4, epistle 2.
26 Commentary on 1 Cor 3; Sermon 20; Commentary on Ps 116.
27 Commentary on Amos 4.
28 Dialogues 4,39.
29 6th Homily on Exodus.
30 Explanations of the Psalms, 37, 3. From Jurgens, William A., ed. and tr., The Faith of the Early Fathers (FEF), 3 volumes, Collegeville, MN: The Liturgical Press, 1979, vol. 3, 17.
31 St. Francis de Sales, CON, 360-362.
32 Ibid., 368-369.
33 Guthrie, D. and J.A. Motyer, eds., The New Bible Commentary, Grand Rapids, MI: Eerdmans, 3rd ed., 1970, 1178. The Lutheran Johannes Bengel (1687-1752), and the Anglican Henry Alford (1810-71), both highly-respected expositors, also held that Onesiphorus was dead.
34 Jamieson, Robert, Andrew R. Fausset, and David Brown, Commentary on the Whole Bible, Grand Rapids, MI: Zondervan, 1961 (orig. 1864), 1376.
35 Robertson, A.T., Word Pictures in the New Testament, Nashville: Broadman Press, 1930, 6 volumes., vol. 4, 615.
36 Sermon: “Holiness Necessary for Future Blessedness,” 1834 (On Hebrews 12:14).
37 Schaff, Philip, History of the Christian Church, vol. 2, “Ante-Nicene Christianity: A.D. 100-325,” 5th ed., New York: 1889; rep. Grand Rapids, MI: Eerdmans,ch. 12, sec. 156, 604-606.
38 New York: Harcourt Brace Jovanovich, 1964, 107-109.