They refers back to those who believed in him (verse 36).

Since this scene takes place in the Temple area, it is possible that the stones referred to were building stones, intended for use in the Temple Herod was having constructed. In 10.31 the people again pick up stones to throw at Jesus, on the accusation that he had made himself equal with God, a charge they equate with blasphemy (verse 33). Here the people’s reaction is prompted by Jesus’ use of the divine name I Am (verse 58), which also would have been interpreted by them as blasphemy, though the charge is not explicitly stated.

Hid himself (many translations) is most probably the meaning of the Greek text, rather than “was not to be seen” (New English Bible; Phillips “disappeared”), which seems to suggest a miracle and at the same time may represent an attempt to avoid making Jesus look cowardly by hiding himself. A few ancient Greek manuscripts expand the text at this point by the additional statement “he walked through the middle of the crowd,” which is definitely an attempt to incorporate a miraculous element into the text. However, there is no suggestion of anything miraculous here or in 12.36, where the same Greek verb occurs.

Quoted with permission from Newman, Barclay M. and Nida, Eugene A. A Handbook on the Gospel of John. (UBS Handbook Series). New York: UBS, 1980. For this and other handbooks for translators see here .