The Jedi Temple lay at the heart of the Star Wars sequel trilogy, and after the Clone Wars it became Palpatine's Imperial Palace. Established a thousand years before the prequel trilogy, the Jedi Temple became the ultimate sanctuary of the entire Order. It had been built atop an ancient Sith shrine, representing the Jedi belief the light side of the Force could cap the darkness, and - although it was based on the galactic capital - the distance from the Senate served as a reminder the Jedi were not supposed to be bound too closely to political matters.
When he initiated Order 66, Palpatine could not resist sending Anakin Skywalker - his new apprentice - to sack the Jedi Temple and slaughter the Younglings being trained there. The Jedi believed Anakin to be the Chosen One, destined to bring balance to the Force by destroying the Sith, but Darth Sidious had turned their Chosen One against them. An egotist to the core, Palpatine believed the Chosen One to be the one had chosen to enact his will. The newly-christened Darth Vader's attack on the Jedi Temple was thus both a test of his allegiance to the dark side and a statement to the Jedi that the Sith had triumphed.
The Jedi Temple Became The Imperial Palace After The Clone Wars
In the aftermath of the Clone Wars, Palpatine transformed the Republic into his own Galactic Empire. The Jedi Temple again became a symbol of this, because he settled in the building as his own home and court. The Jedi Temple - a beacon of light and hope for a thousand years - became Palpatine's Imperial Palace. Palpatine lined its corridors with Sith relics he had collected over the years. These were supplemented by other relics he retrieved from the so-called "Bogan Collection" maintained by the Jedi Archivists, a store of dark side artifacts they kept in the Temple so their darkness would not corrupt the galaxy. Palpatine, of course, studied them and learned all their secrets.
The Jedi Council chambers appear to have become important meeting places for leaders of the Empire, with Wilhuff Tarkin recognizing them in James Luceno's novel Tarkin, set five years after the end of the Clone Wars. It no doubt amused Darth SIdious that these rooms were still the places where the fate of the galaxy was decided, but that now they were used for the purposes of the Sith. The Jedi believed their light would quash the darkness, but Palpatine flaunted his belief that darkness had won.
The Secret Sith Shrine Became The Center Of Palpatine's Power
Meanwhile, Luceno's novel Tarkin reveals Palpatine had droids excavate the ancient Sith shrine beneath the Jedi Temple. This became the center of his power, a sanctuary where he meditated on the dark side of the Force. He initially kept this secret from every living being, even Darth Vader himself, although he planned to let his apprentice in on the secret. "It was here that they would one day work together the way Sidious and Plagueis had to coax from the dark side its final secrets," the book notes. "Such perilous machinations required two Sith, one to serve as bait for the dark side, the other to be the vessel. Success would grant them the power to harness the full powers of the dark side, and allow them to rule for ten thousand years." This probably foreshadows Palpatine's failed attempt to create a Force Dyad with Darth Vader.
It is a mark of the Emperor's evil that, after the Clone Wars, the Jedi Temple became such a place of evil. It's unclear how many Jedi realized Palpatine was a Sith, but those who did would see this transformation as the ultimate demonstration of his victory in Star Wars. This, of course, was just the symbol the Emperor intended to send.
