The first signs of trouble for the Jedi Order came a decade before the Clone Wars, when Qui-Gon Jinn returned to the Jedi Temple with a troubling report from Tatooine. On that forlorn desert planet, Qui-Gon had battled a tattooed warrior skilled in the Jedi arts. The Jedi thought the Sith had been destroyed centuries ago, but Qui-Gon’s encounter suggested they had survived – and might even now be plotting against the Order in secret.

Qui-Gon also had an extraordinary request: He wished to train Anakin Skywalker, a slave boy he’d freed on Tatooine. Qui-Gon believed Anakin was the Chosen One of ancient Jedi prophecy, who would one day bring balance to the Force. The Jedi Council tested Anakin in the Temple, and determined he was indeed strong with the Force. But they refused Qui-Gon’s request. Yoda explained that Anakin was too old to escape emotional attachments during his training, but Obi-Wan Kenobi understood the real reason: The masters sensed something dangerous about the boy.

The Council reluctantly agreed to Qui-Gon’s dying wish, and allowed Obi-Wan to train Anakin. A decade later, an assassination with a mysterious weapon led Obi-Wan to the Jedi Archives in search of information about the planet Kamino. To his surprise, the archives showed no planet at Kamino’s coordinates – someone had erased it from the records.

On Kamino, Obi-Wan discovered an astonishing secret: The planet’s cloners had spent a decade growing and training a clone army – one they said had been requested and paid for by the Jedi Master Sifo-Dyas. This was a surprise to the Jedi Council: No such order had been placed, and Sifo-Dyas was long dead. The Jedi told Obi-Wan to apprehend Jango Fett, the source of the clones, for questioning on Coruscant.

Events elsewhere in the galaxy had reverberations in the Jedi Temple. On Tatooine, Anakin Skywalker gave into his rage and pain, slaughtering the Tusken Raiders that had kidnapped and tormented his mother. Anakin’s emotions sent shock waves through the Force, which Yoda felt in his quarters within the temple.

During the Clone Wars, the daring bounty hunter Cad Bane infiltrated the Jedi Temple’s Holocron Vault, off-limits to all Jedi except Council members because it contained some of the Order’s oldest secrets. Bane escaped with a Holocron, which he had stolen for the Sith Lord Darth Sidious.

A bombing at the Jedi Temple forced the Jedi to confront the growing paranoia of citizens who blamed the Order for the war. But an investigation by Anakin and Ahsoka Tano suggested something even more disturbing: A Jedi might have been involved with the plot.

The evidence pointed to Ahsoka, who was tried by a Jedi tribunal and expelled from the Order. But the real culprit was Barriss Offee. Believing the Jedi had lost their way, Barriss sought to force the Jedi to confront their role in the Clone Wars – and framed Ahsoka as the mastermind of the bombing.

With Barriss’s role revealed, Ahsoka was reinstated and welcomed back to the Jedi ranks. But she refused to return, leaving the Temple and seeking a new path – one that would have fateful consequences for the galaxy decades later.

In the final days of the Clone Wars, Supreme Chancellor Palpatine appointed Anakin as his representative to the Jedi Council. Suspicious of Palpatine, the Jedi Masters accepted the appointment but refused to grant Anakin status as Master. That angered the volatile young Jedi, pushing him into a closer relationship with the Supreme Chancellor.

In the Temple’s war room, the Jedi received word that Obi-Wan had cornered the Separatist warlord General Grievous on Utapau. The masters agreed that if Palpatine didn’t surrender his emergency powers after Grievous’s death or capture, the Jedi Order would have to remove him from office and take over the Senate. Galactic affairs had reached a crisis point.

Anakin discovered that Palpatine was in fact Darth Sidious, the hidden Sith Lord behind the Clone Wars. Mace Windu and a party of Jedi tried to arrest the Chancellor, but Anakin interfered, terrified that Sidious’s death would leave him unable to save Padmé Amidala from the fate he’d foreseen. Anakin pledged himself to the Sith, becoming Darth Vader, and led a force of clone troopers to the Jedi Temple.

Inside the Temple, Anakin and the troops slaughtered all the Jedi they found. Not even the younglings who’d sought refuge in the Council chamber escaped the terrible massacre. Elsewhere in the galaxy, clone troopers obeying Order 66 murdered the Jedi Generals they’d served.

The attack left the Temple in flames and the Order in ruins. A message was sent out from the Temple ordering all Jedi to return – but those who did found themselves captives.

As Palpatine declared that the Republic had been reborn as the Empire, Obi-Wan Kenobi and Yoda fought their way past the clone troopers guarding the Temple. They disarmed the signal luring Jedi back to the Temple and discovered evidence that Anakin had led the assault. Both Obi-Wan and Yoda would become exiles, working in secret to resurrect the Order they’d served.