The temple needed to be cleansed. So do our hearts, which are now the dwelling place of God.

The temple in Jerusalem was the place where God had said to His people, in essence, "if you want to find Me, this is where to come". But it had become a place where people were cheated out of their money and offerings in the name of God. That's why Jesus needed to drive the purveyors of this filth out.
But there was more going on that simply a kind of purification; the temple itself was only a sign. It wasn't "the thing", but a sign that pointed to "the thing". Or rather, to "the One".
John's early chapters are known as The Book of Signs, as John says over and over that the things Jesus were doing were signs that pointed to Himself. We often think of the miracles—which certainly were signs—but the temple was another one too. It was something that ultimately pointed to Jesus, and that's why He could be so confident in saying that He could raise it up in three days if it was destroyed: because He was talking about "the thing"—His very own body—and not the sign.
And now, the Christian Church is the new temple, the new place where God has said, in essence, "if you want to find Me, this is where to come". But I'm not talking about buildings; the Church is the people of God gathered around His Word and Sacraments, whatever building they're in. Just like the Apostle Peter says, we also, "like living stones, are being built into a spiritual house to be a holy priesthood, offering spiritual sacrifices acceptable to God through Jesus Christ." (1 Peter 2:5)
The season of Lent is a season of cleansing, not of the physical buildings, but of the living stones that are the new temple: our hearts. Jesus cleanses our hearts with His powerful word, just like He cleansed the temple in Jerusalem.
And that is a very, very good thing.
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