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When Peter and John arrived at Jesus' tomb, it was light enough for them to see inside, unlike Mary's first visit. Remember that Nicodemus and Joseph of Arimathea had wrapped Jesus' body in linen cloths along with myrrh and aloes weighing about 100 pounds (19:39). Jesus' body was wrapped like a mummy. When Peter and John later peered into the tomb on that first Easter morning, all they would have seen was the collapsed shell of the linen wrappings. They had no doubt that Jesus was alive. If His body had been stolen, the wrappings would have been unwrapped or missing. So they "saw and believed" (20:8).
By His own testimony to Mary (20:17), Jesus had not yet ascended to His Father since His death and resurrection. So where was His spirit while His body was lying in the tomb? Jesus told the repentant thief on a cross beside Him, "Today you shall be with Me in Paradise" (Luke 23:43). If Jesus had not yet ascended to His Father, but went to Paradise, it seems that there must have been a place of paradise that was not heaven. We also know that Scripture states that after His death, Jesus descended "into the lower parts of the earth" (Eph. 4:9). Jesus also declared that He would spend "three days and three nights in the heart of the earth" (Matt. 12:40). In the story of the Rich Man and Lazarus (Luke 16:19-31), Jesus spoke of a place that seems as if it might be a paradise in the heart of earth, adjacent to Hades, where the righteous lived after death. I only wish we had a few more verses of Scripture that gave us certain insight into this!
During His first appearance to His disciples on the evening of His resurrection, Jesus breathed on them and said, "Receive the Holy Spirit" (20:22). Some say this is when the disciples were born again (even though they were already "saved" in the sense of being forgiven). Others say it was a foreshadowing of their being baptized in the Holy Spirit, the fulfillment of which was about 50 days later on the day of Pentecost.
Jesus also told them, "If you forgive the sins of any, their sins have been forgiven them; if you retain the sins of any, they have been retained" (20:23). It is difficult to believe that Jesus was giving them the authority to decide who would be forgiven and who would not, as it would seem as if that would be stepping into God's sole domain. Thus I think Jesus likely meant that they were to carry the message of forgiveness to everyone. Whoever accepted it would be forgiven, and whoever didn't would not. This interpretation certainly harmonizes with the rest of the New Testament.
Personally, I'm glad Thomas doubted, as his being persuaded that Jesus had been resurrected bolsters my own faith. To trust the report of naive people is risky, but when a skeptic does his investigation and is convinced, that gives us more reason to believe. Although most of us have not seen Jesus since He was resurrected, it is good to know that at least 500 eye-witnesses did see Him alive not long after His resurrection (1 Cor. 15:6). And, as Jesus said, blessed are we who have not seen Him, "yet believed" (20:29).
What a frustration it is to read 20:23: "Therefore many other signs Jesus also performed in the presence of the disciples, which are not written in this book." How I wish John had recorded them! John felt, however, that he had mentioned a sufficient number of Jesus' signs in order to achieve his purpose: "But these have been written so that you may believe that Jesus is the Christ, the Son of God; and that believing you may have life in His name" (20:31). Incidentally, that is one more verse that indicates God's universal offer of salvation. John believed that any and all of his readers, current and future, could believe in Jesus and receive eternal life. (I'll bet you were hoping we could go one day without my refuting Calvinism! So sorry! I just couldn't resist!)