The story begins with an amnesiac Ezra waking up outside the remains of a crashed Star Destroyer on a mysterious planet. As he attempts to figure out what's going on, he encounters a certain Chiss Grand Admiral who also suffers from similar memory problems. As the duo try to solve the mysteries of their pasts, they must learn to trust each other if either hopes to make their way back to civilization.
After completing the story, the author also wrote a bonus story called Star Wars: Uncharted Stars - The Rise of Skywalker Bonus Story, which follows the Rebels characters during the events of The Rise of Skywalker.
Star Wars: Uncharted Stars provides examples of:
- Adaptation Deviation: In Star Wars Legends, the Outbound Flight was a vessel made up of six Dreadnaught-class heavy cruisers sent by the Old Republic to colonize another galaxy. This version of the Outbound Flight is a Chiss expansionary ship.
- Adaptational Origin Connection: This version of the Yuuzhan Vong has their species originate from Myrkr, explaining their immunity to the Force, and reveals that the Chiss were responsible for their mutated appearance.
- Amnesiac Hero: Both Ezra and Thrawn suffer from amnesia at the start of the story. Ezra is unable to remember any details of his past, while Thrawn forgets everything prior to joining the Empire.
- Earn Your Happy Ending: After years of battling the Empire and the Yuuzhan Vong, Ezra is finally able to return to the main galaxy and happily reunites with his former Ghost crewmembers.
- Entertainingly Wrong: After witnessing Ezra's Force powers, the surviving Imperials from the Chimaera assume Ezra is an Inquisitor sent to help Thrawn.
- Gadgeteer Genius: Thrawn's niece Tharin is a Chiss scientist who developed the Chiss Clawcraft (a Chiss version of the TIE Defender) and electro-lances (a lance version of the lightsaber).
- Interspecies Romance: One eventually develops between Ezra, a human, and Tharin, a Chiss.
- Mythology Gag: There are many references and nods to the Legends continuity.
- The planet Ezra and Thrawn are stranded on at the beginning of the story is Myrkr and the creatures they encounter are ysalamiri and vornskrs.
- Both Abeloth and Darth Krayt appear as major antagonists in the story.
- Chiss Clawcraft are shown to be used by the Chiss.
- The Yuuzhan Vong are the main antagonistic faction of Uncharted Stars and they make exclusive use of Organic Technology.
- The Vagaari play a role in the story as a Slave Race to the Yuuzhan Vong.
- Punch-Clock Villain: The surviving Imperials from Thrawns ship are all shown to be fairly decent people.
- Shipper with an Agenda: It's later revealed that Thrawn, being a Manipulative Bastard, intentionally assigned his niece Tharin to work with Ezra in the hopes that the two would fall in love, thereby giving Ezra a reason to continue working for the Chiss Ascendancy.
- What the Hell, Hero?:
- Ezra deliver a massive one to Thrawn after regaining most of his memories and realizing that almost everything Thrawn told him about his past was a lie.
- Ezra gives another one to Thrawn after reuniting with Sabine and discovering that Thrawn had also lied about the Ghost crew dying in the fuel depot explosion on Lothal.
- Year Inside, Hour Outside: It turns out that due to the purrgil traveling near a black hole, the gravitational anomalies caused the crew of the Chimaera to experience time at a much slower rate compared to the rest of the galaxy. When Ezra and Thrawn are finally rescued by the Chiss, they learn that they had been missing for 8 months.