The Fall of the Jedi is the era the prequel films occupy, and it is the richest shelf in Star Wars for anyone who likes institutional decay. The best books here are not about lightsabers. They are about a bureaucracy that cannot see the shape of its own failure, and about individual Jedi who sense something is wrong and lack the vocabulary to name it.
The state of the Order
By 32 BBY the Jedi have been the Republic's peacekeepers for so long that the two roles have fused. They answer to the Senate. They carry diplomatic credentials. They have a seat at the table and, crucially, an institutional stake in the table remaining where it is. The High Republic books make this visible in retrospect: the Order that fights the Nihil is not the Order that fails to notice Palpatine, and the difference is two hundred years of being needed slightly less each decade.
The Council's specific blind spot is prophecy. It has an archive full of it and an official position that it is unreliable. Claudia Gray's Master & Apprentice, set roughly eight years before The Phantom Menace, is built entirely on that argument, and it refuses to make either side stupid.
The political engine
Palpatine's plan is not complicated, which is why it works. Manufacture a crisis the Senate cannot resolve. Be the reasonable man in the room. Accept emergency powers reluctantly. Manufacture a war that requires the Jedi to become generals, so that when they are killed the galaxy reads it as a military purge rather than a religious one. Every step is legal. The Republic is not overthrown; it votes.
What to read and in what order
Start with Master & Apprentice — it is the most welcoming door on the whole shelf, assumes nothing, and explains itself as it goes. From there the era divides into the pre-war political material and the enormous Clone Wars shelf, which this site treats as its own period; see The Clone Wars.
Canon and Legends
This era exists twice. The Legends version has its own extensive Clone Wars publishing programme, its own Jedi apprentice series, and the Genndy Tartakovsky micro-series. The canon version replaced almost all of it from 2014 onward. Where a Legends book is worth reading anyway, this site says so and tags it clearly — but for the prequel era specifically, the canon material is the stronger shelf, which is not true everywhere.
The era ends with Order 66 and the Declaration of the New Order, both in 19 BBY and both within hours of each other. What follows is Reign of the Empire.