The story in John 20:1-18 reveals that Mary Magdalene and the disciples, including Peter, did not anticipate the tomb to be empty. This makes us realize how shocking it must have been for them to see it empty that morning. Mary Magdalene, who had been possessed by seven demons (Luke 8:2) and stood with Jesus' mother during his crucifixion, returns to the tomb before dawn on the first day of the week. She is surprised to see the stone has been moved from the tomb. As a result, she ran to Peter and another disciple, who may have been John, and told them that someone had taken Jesus' body to an unknown location. She did not seem to consider that he might have been resurrected.

Peter and the beloved disciple ran to the tomb, but the beloved disciple was faster and arrived first. He saw the grave linen clothes but did not enter. Peter arrived and went inside the tomb. He saw the grave clothes and a folded face cloth. The beloved disciple also entered the tomb and believed after seeing it. It seems that Peter and John (referred to as "the disciples") returned to join the other disciples who were already gathered.

After Peter and John departed from the tomb to join the other disciples, Mary remained behind, crying and peering inside. She noticed two angels in the spot where Jesus' body had been placed—one at the top and one at the bottom. When Mary saw Jesus, she did not recognize him initially (v.14). This suggests that Jesus' resurrected body appeared more like an ordinary human than an angel since Mary distinguished the angels but mistook Jesus for the gardener when she spoke to him. Jesus inquires about the reason for her weeping and the person she is searching for. In verse 16, Jesus calls out her name, and she immediately recognizes him and acknowledges him as her teacher. The fact that John includes the Semitic word "Rabboni" and translates it suggests that Mary addresses Jesus with a strong sense of intimacy, devotion, and affection. Jesus tells Mary not to hold onto him tightly as he has not yet ascended to the Father. She cannot cling to him permanently because he is returning to the Father. Jesus sends Mary to his "brothers," showing that he does not bear any resentment toward them. Even though the followers of Jesus had abandoned him and Peter had denied he was his disciple, Jesus referred to them as his brothers and sent Mary to them.

In verse 19, John describes how Jesus surprised the disciples by appearing among them and speaking words of peace. Despite the doors being closed, Jesus stood alive and well in their midst. After comforting the disciples, Jesus provides physical evidence of his suffering and resurrection by showing them his hands and side (v. 20). This convinces the disciples, lifting their spirits from sadness to joy. Jesus has brought peace to their hearts and assurance of his resurrection to their minds, leading to their joy. Jesus spoke to his disciples about peace and how they will introduce God to people who don't know Him. The disciples will offer forgiveness through Jesus and welcome others into their community. They will also distinguish themselves from the world to show that those outside the church are outside Christ and will stand before God unforgiven.

Thomas was not with the disciples when Jesus appeared and spoke to them after his resurrection; he doubts their claim of seeing him. In verse 25, Thomas expresses his desire to be convinced of Jesus' resurrection by physically touching his wounds, just like the other disciples did in verse 20. The disciples, including Thomas, gathered behind locked doors when Jesus appeared and offered them peace. A compassionate Jesus did not scold or rebuke Thomas for his doubts but invited him to touch his wounds and believe. Jesus blesses those who believe without having to see like Thomas did (verse 29). Jesus is not criticizing Thomas for needing proof but praising those with faith. This message proclaims the blessing for those who believe in Jesus without seeing him (similar to 1 Peter 1:8 and Revelation 1:3).

John's statement that "Jesus did many other signs in the presence of the disciples, which are not written in this book" commends the other Gospel accounts and other verbal testimony from the disciples. John is not claiming an exclusive version of what Jesus did. Comparing John's account to those of other disciples is not necessary. John chose which events to include for a specific reason, as mentioned in verse 31—Jesus is the King, the Messiah, the Son of God.