There are several stories told throughout the three books. The main plot is that of Exar Kun's spirit attempting to turn Luke's trainee Jedi, he kills one of them and turns Kyp Durron who goes on a rampage with the Sun Crusher. The Jedi trainees eventually destroy Kun and Kyp is brought back to the light by his friend Han Solo.
The later novel I, Jedi is a retcon of much of the action at the Jedi Academy, inserting Corran Horn into the storyline and smoothing out parts that do not conform to later continuity.
In the original outline for the Jedi Academy Trilogy Mon Mothma would have died as a result of her infection, but Lucasfilm ultimately rejected this idea.
In November of 1994, to promote the upcoming release of the Science Fiction Book Club edition of the Jedi Academy trilogy in an omnibus hardcover, the series publisher, Bantam Spectra, released a TV commercial for the series.