There are three events where only three of the disciples (Peter, James, and John) was with Jesus – raising of Jairus’s daughter from the dead, Jesus’s transfiguration, and the prayer at Gethsemane.
Mar 5:35-37 While he yet spake, there came from the ruler of the synagogue’s [house certain] which said, Thy daughter is dead: why troublest thou the Master any further? 36 As soon as Jesus heard the word that was spoken, he saith unto the ruler of the synagogue, Be not afraid, only believe. 37 And he suffered no man to follow him, save Peter, and James, and John the brother of James.
Luk 9:28-29 And it came to pass about an eight days after these sayings, he took Peter and John and James, and went up into a mountain to pray. 29 And as he prayed, the fashion of his countenance was altered, and his raiment [was] white [and] glistering.
Then cometh Jesus with them unto a place called Gethsemane, and saith unto the disciples, Sit ye here, while I go and pray yonder. And he took with him Peter and the two sons of Zebedee, and began to be sorrowful and very heavy.
All three of these events are recorded in each of the synoptic gospels. However, none of these are mentioned in the fourth gospel. If John was one of the three chosen ones to participate at these major events, why did he not mention them if he wrote the fourth gospel?
Another major event was the raising of Lazarus from the dead. However, this event is only mentioned in the fourth gospel.