Eli dies, explaining why he doesn't seem to present in Rebels.
And either Thrawn shrugs it off and moves on, or it's one of the few topics that makes him Not So Stoic if it ever gets brought up because his death was one of his greatest failures, if not the greatest.- Jossed. Considering the book takes place over a span of years and thus he wouldn't always be a young officer, he ends the book as a commander, so he's off doing other things.
- Double Jossed, as at the end of the book, Eli leaves the Empire and joins the Chiss Ascendancy, so he's in the Unknown Regions.
The threats in the Unknown Regions are Snoke, the Yuuzhan Vong, and/or the Eternal Empire.
The reason Thrawn is not present during the events of the Original Trilogy is not that he's dead, but that he's been recalled as the book reveals his "exile" was actually staged to plant Thrawn in the Empire and he's not truly banished.
- Jossed. He and Ezra went missing after purrgils hyperspace-jumped them to an unknown location. Their fates post-Rebels are currently unknown.
If it does become a trilogy, the final book will deal with post-Rebels events
Namely, whatever Thrawn and Ezra went when they jumped and why neither of them could return.