With the beginning of the Empire came intensified persecution of the Jedi. The animosity they had suffered from the Separatist systems before the Clone Wars now spread to most systems. Bounties became more and more common, Jedi were turned away from and denied help from an increasing number of systems. When Imperial troops started hunting Jedi, it became clear who the real enemy was. With an Imperial presence in almost every system in the Galaxy, most Jedi went into hiding.

Through espionage, and contacts within the Senate, the surviving Jedi become certain of what they already suspected, that the Emperor was a Sith Lord. The Jedi and their few remaining supporters believed that the only way to restore peace to the Galaxy, was to kill the Emperor. Several attempts were made on his life, by Jedi and those sympathetic the Old Republic, but the Emperor was too well protected on the Imperial Homeworld. It would be necessary to lure him away if they were to have any chance of success.

When several systems rebelled against Imperial rule, some of the Jedi believed an opportunity had presented itself. Several of the best Jedi generals and pilots joined the rebellion in prominent, highly visible positions. Their abilities helped the rebelling systems repel the Imperial attacks. As the revolt dragged, the Emperor became more impatient with his commanders, finally taking command of the besieging forces himself. Determined to crush the rebellion and kill the Jedi leading it himself, he didn't realize that it was a trap set for him. In the first battle after he had joined the Imperial forces, a group of Jedi penetrated the Imperial lines, boarded the flag ship and fought their way to the bridge. Here the Jedi were only defeated because one of their own number betrayed them.

Without the Jedi, the uprising was soon crushed. With its end, came the true end of the Old Republic. With one of their own now leading the Imperial death squads, there were few places the surviving Jedi could hide. They were systematically hunted down and killed.