John 20
1 Early on the first day of the week, while it was still dark, Mary Magdalene went to the tomb and saw that the stone had been removed from the entrance. 2 So she came running to Simon Peter and the other disciple, the one Jesus loved, and said, “They have taken the Lord out of the tomb, and we don’t know where they have put him!”
3 So Peter and the other disciple started for the tomb. 4 Both were running, but the other disciple outran Peter and reached the tomb first. 5 He bent over and looked in at the strips of linen lying there but did not go in. 6 Then Simon Peter came along behind him and went straight into the tomb. He saw the strips of linen lying there, 7 as well as the cloth that had been wrapped around Jesus’ head. The cloth was still lying in its place, separate from the linen. 8 Finally the other disciple, who had reached the tomb first, also went inside. He saw and believed. 9 (They still did not understand from Scripture that Jesus had to rise from the dead.) 10 Then the disciples went back to where they were staying.
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24 Now Thomas (also known as Didymus [ a ] ), one of the Twelve, was not with the disciples when Jesus came. 25 So the other disciples told him, “We have seen the Lord!”
But he said to them, “Unless I see the nail marks in his hands and put my finger where the nails were, and put my hand into his side, I will not believe.”
26 A week later his disciples were in the house again, and Thomas was with them. Though the doors were locked, Jesus came and stood among them and said, “Peace be with you!” 27 Then he said to Thomas, “Put your finger here; see my hands. Reach out your hand and put it into my side. Stop doubting and believe.”
28 Thomas said to him, “My Lord and my God!”
29 Then Jesus told him, “Because you have seen me, you have believed; blessed are those who have not seen and yet have believed.”
30 Jesus performed many other signs in the presence of his disciples, which are not recorded in this book. 31 But these are written that you may believe [ b ] that Jesus is the Messiah, the Son of God, and that by believing you may have life in his name.
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Notice verse 2....they took the Lord's body and we don't know what they did with him.
Verse 9...they still didn't fully understand the sacrifice and resurrection.
It's important to remember we have the written gospel accounts to reflect on and get a clearer picture. Those living at that time didn't have this advantage of being able to sit back and try to see the whole picture. How many times did Jesus have to repeatedly tell his associates that he would be killed? They had trouble based on their own expectations of what the Messiah was going to be like.
I don't see anything that gives me the idea that Thomas didn't believe Jesus was the Son of God or that God has the power to raise from the dead. Given verse 2 (and that we know others wanted the body of Jesus guarded due to the fear that people would steal it away to make it look like he wasn't dead), I find it more likely that Thomas wanted to make sure it really was Jesus and not someone attempting to impersonate him for self glorification.