The “resurrections” to which Christ is referring in John 5:28-29 should be interpreted in light of verse 25 of this chapter. There, we read, “Truly, truly, I say to you, an hour is coming, and is now here, when the dead will hear the voice of the Son of God, and those who hear will live.” Christ links the then-present and ongoing spiritual vivification of those who are said to be “dead” (v. 25) with a then-future event in which these very same people (whom he categorizes as “those who have done good” and “those who have done evil”) will come out of “the tombs” (v. 28). Those of whom Christ spoke (i.e., those who were passing “from death to life” in response to hearing his voice at that time – see verse 24) were not literally dead. The “death” in view in vv. 24-25 is a figurative “death” (i.e., “dead in transgressions and sins”). In verses 28-29, Christ is simply building off of his already-established metaphor of death and resurrection, and referring to the consummation of what had already begun to take place due to the proclamation of the gospel.
In verse 27, Christ is referring to that which was yet future when he says “the hour is coming,” and to that which was still present when he says “and is now here…” He says “and is now here” because this figurative “resurrection” had already begun taking place, and was to continue and culminate at a yet-future time. Throughout John’s gospel, Christ uses the phrase “an hour is coming” in reference to a time that was in the relatively near future. In John 4:21-23 we read,
“Woman, believe me, the hour is coming when neither on this mountain nor in Jerusalem will you worship the Father. You worship what you do not now; we worship what we know, for salvation is from the Jews. But the hour is coming, and is now here, when the true worshipers will worship the Father in spirit and truth, for the Father is seeking such people to worship him.” John 4:21-23
Similarly, we read later in chapter 16:
They will put you out of the synagogues. Indeed, the hour is coming when whoever kills you will think he is offering service to God…But I have said these things to you, that when their hour comes you may remember that I told them to you…I have said these things to you in figures of speech. The hour is coming when I will no longer speak to you in figures of speech but will tell you plainly about the Father… Behold, the hour is coming, indeed it has come, when you will be scattered, each to his own home, and will leave me alone. Yet I am not alone, for the Father is with me. John 16:2-4, 25, 32
As used in the above passages, the expression “the hour is coming” evidently refers to the period of tribulation and persecution leading up to, and climaxing in, the overthrow of the Jewish nation in 70 AD. Jesus adds “the hour is now here” because what he was referring to had already begun, and would continue until and culminate in, the hour that was still “coming” (which, by the time the apostle John wrote his first epistle, had already drawn near – see 1 John 2:18). Those who were “passing from death to life” in v. 25 are the same persons who would later come out of their “tombs” at the future time in view, to receive either “life” or “judgment.”
If these verses are understood literally, however, then they actually prove too much. If “the tombs” of which Christ speaks (v. 28) refer to literal tombs, then Christ would be saying that only those who are in literal tombs will be raised (for he doesn’t say anyone else will be). But what about all the literal dead who weren’t placed in tombs? What about all the dead who weren’t buried at all? A literal interpretation of Jesus’ words in vv. 27-28 is simply not tenable, and disregards the immediate context. The “dead” of whom Christ is speaking are not literally dead (no more so than the “dead” of whom Paul speaks in Eph 2:1 and 5:14, and of whom Peter speaks in 1 Pet 4:6), nor are the “tombs” literal tombs (no more so than the “graves” of which we read in Ezekiel chapter 37, when God declares, “Behold, I will open your graves and raise you from your graves, O my people.”). The people of Israel are likely represented by Christ as being in “tombs” to more forcibly represent their low and undesirable condition of sitting “in darkness and in the shadow of death” (Luke 1:79). But as the gospel was being proclaimed throughout Judea, multitudes were responding to it in faith, and were consequently being enlightened with the truth of the gospel and receiving “life.”
This passing from death to life (cf. Eph 2:1, 5-6) continued throughout the ministry of the apostles, even up until the time when the city of Jerusalem and the temple were destroyed by the Romans (something John reveals was greatly feared by the Jewish leaders at that time – see 11:48-50). Among those who believed the gospel, some (“many,” according to John 12:42-43) did not confess their belief for fear of what others would think, and because they didn’t want to be “put out of the synagogue.” Thus, while they were awakened to the new life of the gospel, they either failed to go public with their faith, or ultimately “fell away” from the truth of the gospel altogether and returned to their former way of life (see Heb 2:3, 6:4-8; 10:26-29; John 8:30-33, 37, 44; 2 Pet 2:20-22; etc.). If any among the people of Israel “fell away” from the truth of the Gospel at some point prior to Christ’s coming in his kingdom (and thus did not “endure to the end” as Christ exhorted his followers to do in order to be “saved”), they exposed themselves once again to the coming judgment upon their nation. Christ himself warned his disciples, “If anyone does not abide in me he is thrown away like a branch and withers; and the branches are gathered, thrown into the fire, and burned” (John 15:6). Christ is here talking about those who had “passed from death to life” and were abiding in him (cf. John 6:54, 56), but subsequently fall away from the faith. It is these people who were “resurrected to judgment” when the “hour” came. Having “fallen away from grace,” they were consequently judged with the rest of the nation when Christ came to establish his kingdom in the world, and found themselves awakened not to “life” but to the “shame and everlasting contempt” prophesied in Daniel 12:2. (I find it is significant that Paul, in Eph 5:14, combines the metaphors of “sleeping” and “awakening” found in Daniel 12:2 with that of being “dead” and “arising,” and applies it to circumstances taking place in his day).