This is one of the four Saga-based games that I run on the Saga-Edition.com board. Its Out-of-character (OOC) thread may be read here. The In-character (IC) thread for the first episode, Into the Flames, is located here.
This game is an Infinity, the premise of which is:
The party contains a total of five PCs, three of which are Jedi.
Anakin Skywalker arrives a few seconds too late to stop Mace Windu from killing Palpatine. In his rage at the loss of what he believes is the only means by which his wife might be saved, he kills the Jedi Master by hurling him out the window using the Force. Skywalker assumes command of the Grand Army of the Republic and initiates Order 66. Consumed by the Dark Side, he and the 501st Legion then kill everyone in the Jedi Temple. Meanwhile, General Grievous kills Obi-wan Kenobi on Utapau before Order 66 is received. Grievous then escapes to continue leading the CIS. Yoda kills Skywalker in the Senate building. Bail Organa becomes Supreme Chancellor in an emergency session of the Senate.
The Separatists obliterate Tipoca City by orbital bombardment, ending clone production. Less than six months later, Coruscant falls to the ever-increasing might of the Separatist droid armies, as does Alderaan and many other worlds. Without replacement clones, the Army of the Republic cannot sustain escalating battle losses. Grievous declares himself Emperor after eliminating a couple of CIS leaders and several Republic senators. This example is not lost on outspoken senators like Mon Mothma and Garm Bel Iblis, who flee and join Bail Organa, Padme Amidala (and her twins), and the remnants of the Republic navy out in the Rim Territories. A much-reduced Jedi Order led by Yoda scatters as the Empire mercilessly hunts them down.
The Clone Wars segues directly into the Galactic Civil War, with the Alliance to Restore the Republic fighting an insurgency against the new Empire. What would normally be 19 BBY in a canon timeline becomes year zero of the Imperial Era (0 IE). The campaign begins two years later (in 2 IE). The galaxy remains fractured and ablaze. Many sectors continue to openly resist the Empire, and with the bulk of what used to be the Republic navy under rebel control, the Empire is far from having the iron grip on the galaxy it would have had under the rule of Sith lords.
The Rebel fleet does contain clones. On the few ships that have both Jedi and clones aboard, relations are frigid between them. While the clones hold no antipathy for surviving Jedi (the clones were just following orders), the Jedi, understandably, do not trust clones after troops that had been thought to be honorable turned on their commanders. The Jedi Order was betrayed, and most Jedi will not work with clones, viewing them as less human than a protocol droid. At least droids are loyal.