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I believe that Joseph of Arimathea took the body of Jesus to his residence in Jerusalem and there with Nicodemus, Mary Magdalene, and Jesus' mother Mary a plan of action was decided on which consisted of leaving Jesus' body at his residence while he took the linen he had wrapped Jesus in to his personal tomb  and left it in there and then sealed the tomb with a large stone. Then they went back to Joseph's home and waited for Jesus' body to be resurrected as Jesus had said he would be. After Jesus' body began to rot it became apparent that something had to be done and Joseph buried Jesus on his property.

When the persecution of Christians began Joseph, Nicodemus, and Mary Magdalene fled Jerusalem but not before re-burying Jesus' bones in a container in a nearby graveyard which later became known as a Christian graveyard.  In 1946 the container was unearthed. On the container was written the name of Jesus with a prayer in Aramaic for god to resurrect the two bodies. Yes there were bones from two different people in the container. As to who the bones of the second occupant belonged to I had thought that maybe it was Joseph trying to piggyback to heaven with Jesus but it appears Joseph left Jerusalem never to return several years after Jesus death. Since Mary, the mother of Jesus, didn't leave with Joseph maybe she had died before Joseph left and it is her bones that were buried with the reburied bones of Jesus.

I don't believe this theory contradicts the New Testament other than claims that 500 people saw Jesus walking around after his death and the supposed eye witness account of Jesus rising into heaven and being seated at the right hand of God. In my opinion these entries were added by early church fathers in an attempt to buttress the Christian case. The early church's insecurity was shown by their offer of forgiveness of sins and entry into heaven for anyone who believed in the resurrection.