Star Wars: Rebels' dramatic finale has just been subtly rewritten by Timothy Zahn's Star Wars novel Thrawn Ascendancy: Lesser Evil - setting up a very different fate for Grand Admiral Thrawn and Jedi Padawan Ezra Bridger. The dramatic Star Wars Rebels season 4 finale saw Ezra outsmart the Chiss Grand Admiral, using the Purrgils (AKA Space Whales) to wreck Thrawn's fleet. The Purrgils jumped into hyperspace, taking Thrawn's flagship with them - with Ezra aboard. Lothal was freed from the Empire, but at a terrible cost to the Rebels. Grand Admiral and Jedi Padawan alike were lost in the depths of the Unknown Regions.
The fate of Thrawn and Ezra has remained a mystery, albeit one Lucasfilm seemingly intends to explore. Thrawn appears to have avoided returning from the Unknown Regions for some years, arriving in the Outer Rim shortly before The Mandalorian season 1. There are hints in season 2 that Thrawn is the one secretly organizing an Imperial remnant who are building up their forces in the Outer Rim; ex-Jedi Ahsoka Tano is aware of his activities, and she's hunting him down in the hopes of finding out what happened to Ezra. After 30 years, Thrawn is once again key to Star Wars' future, because the Chiss Grand Admiral is being set up as the major Imperial threat in the time-period of The Mandalorian, Ahsoka, and presumably also The Book of Boba Fett. Lucasfilm Publishing has commissioned celebrated author Timothy Zahn, the man who created Grand Admiral Thrawn for the old Expanded Universe, to tell Thrawn's canon backstory - and the final book in the series, Thrawn Ascendancy: Lesser Evil, features a major twist that potentially changes everything.
Grand Admiral Thrawn had previously been believed to be a Chiss exile, recruited by the Empire and now loyal to their philosophy. In reality, it seems his exile was contrived by Chiss military leaders precisely for the purpose of getting him into the Empire. Thrawn's mission was twofold; he was to investigate the newborn Empire, assessing them as a potential ally against the myriad threats of the Unknown Regions, and to send allies back to the Chiss. He was never loyal to the Empire at all, instead only ever viewing them as a tool to be used to protect the Chiss, and in fact he always intended to return to the Unknown Region in the end.
This significantly rewrites the end of Star Wars Rebels, in that it offers a potential explanation for Thrawn's failure to return immediately to the Empire. He may not have intended to travel to the Unknown Regions via Purrgil, but in reality he seems to have stayed with the Empire a lot longer than he intended to. Ezra's Purrgil strategy would have left Thrawn in the Unknown Regions once again, and instead of returning to the Empire he presumably decided to complete his real mission by heading back to the Chiss. The Empire would have believed his ship lost in hyperspace, meaning he had the perfect excuse for being missing should he ever seek to return to the wider galaxy.
Ezra's presence, too, becomes rather more significant in light of Zahn's latest trilogy. The Unknown Regions is rife with navigation hazards, and it can be best charted by Force-sensitives using a technique the Chiss call "Skywalking." Rather than remain enemies, Thrawn and Ezra could well have forged an alliance to survive the Unknown Regions - one that saw Ezra then choose to remain with the Chiss. The interesting question, though, is why Thrawn would then return to the Empire several years after Return of the Jedi; it's possible he's not actually planning to go up against the New Republic at all, but that instead the Chiss are facing a threat in the Unknown Regions that demands new resources. If that's the case, future Star Wars shows could go in a very unexpected direction indeed.