Unlike the Synoptic gospels, John mentions the cleansing of the Temple by Jesus in the beginning of his gospel as well as at the beginning of Jesus’ public ministry. The Temple event in John has two parts: the declaration of the impurity of the Temple and the prediction of the new Temple.
Jesus is acting here with the Spirit of Jeremiah (Jer 7, 11). The violence implied here is in the external sense, practically impossible, but symbolically shows the prophetic zeal of Jesus. It is the realization of the situation of the new Temple prophesied by Zechariah 14, 21: “And there shall no more be traders in the house of the Lord of hosts on that day.” Psalm 69, 8 is also cited in the context with a Johannine adaptions of the past tense into future to refer to the passion of Jesus as a result of his zeal for the house of the Father.
Then Jesus predicts the new Temple which is misunderstood by the Jewish leaders. Jesus is referring to his own body and not to the physical temple structure. It has relation to the paschal Mystery through which the new Temple will be revealed. The 46 years, the Jews refer to have been interpreted both in relation to Jesus and the Temple. That it refers to Jesus’ age is not probable. The year agrees rather with the period of reconstruction work begun by Herod the Great in the year 19 BCE. Now when Jesus is in the Temple it is more or less 28 CE. It would be then around 46 years.
The chapter two of John is a preparation of the synthesis of Jesus’ ministry geographically spread out from Galilee to Jerusalem; and theologically consisting of “taking away” and “filling up.” This is a preparation for the narration beginning in Chapter three with the dialogue between Jesus and Nicodemus. Jesus, thus reveals, what is to be and how is to be “taken away” and with what and how “to be filled up.”