The New Jedi Order

The New Jedi Order Series
Two decades after Return of the Jedi, the galaxy is invaded from outside by the Yuuzhan Vong - vicious, pain-loving aliens who use nearly-unstoppable organic technology and are mysteriously invisible to the Force. The whole galaxy will have to unite, friends and enemies alike, if the devastating invasion is to be reversed. The newly re-established Jedi Order, led by Master Luke Skywalker, is front and center in the grueling and heartbreaking war, with Han and Leia's newly adult offspring among the star players.

The longest and most epic Star Wars novel series ever written, The New Jedi Order includes the deaths of several major characters, and sets the stage for a new era of the galaxy's future.

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(Full Series for Kindle)
Vector Prime by R.A. Salvatore
Dark Tide I: Onslaught by Michael Stackpole
Dark Tide II: Ruin by Michael Stackpole
Agents of Chaos I: Hero's Trial by James Luceno
Agents of Chaos II: Jedi Eclipse by James Luceno
Balance Point by Kathy Tyers
Edge of Victory I: Conquest by Greg Keyes
Edge of Victory II: Rebirth by Greg Keyes
Star by Star by Troy Denning
Dark Journey by Elaine Cunningham
Enemy Lines I: Rebel Dream by Aaron Allston
Enemy Lines II: Rebel Stand by Aaron Allston
Traitor by Matthew Stover
Destiny's Way by Walter Jon Williams
Force Heretic I: Remnant by Sean Williams & Shane Dix
Force Heretic II: Refugee by Sean Williams & Shane Dix
Force Heretic III: Reunion by Sean Williams & Shane Dix
The Final Prophecy by Greg Keyes
The Unifying Force by James Luceno

This is a post-Return of the Jedi series from the Legends timeline. Think of it as an alternate universe from the sequel movies and newer books. 

Dark Nest

The Dark Nest Trilogy by Troy Denning
When the ancient insectoid Killiks re-emerge in the Unknown Regions after the Yuuzhan Vong war, the Galactic Alliance, the Jedi, and the Chiss empire are drawn into a complex and multi-sided war. Several young Jedi Knights are absorbed into the Killik hive mind, while Luke and Leia discover previously unknown information about their mother, Padmé Amidala.

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The Joiner King
The Unseen Queen
The Swarm War

This is a post-Return of the Jedi series from the Legends timeline. Think of it as an alternate universe from the sequel movies and newer books. 

Legacy of the Force

The Legacy of the Force Series
Troubled by visions of darkness, war-scarred Jedi Jacen Solo is hellbent on ensuring a better future for his young daughter. As the Alliance descends into a new civil war pitting heroes of the rebellion against each other, Jacen will do anything to bring peace and order to the galaxy: even if it means seizing power as a dictator, joining the Sith, and bringing about the destruction of the Solo and Skywalker families. A tragic tale of the dangers of power and self-assuredness.

In an ongoing side plot, Boba Fett leads a new generation of Mandalorian warriors, but he too struggles with family issues rooted deep in his shameful past.

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Betrayal by Aaron Allston
Bloodlines by Karen Traviss
Tempest by Troy Denning
Exile by Aaron Allston
Sacrifice by Karen Traviss
Inferno by Troy Denning
Fury by Aaron Allston
Revelation by Karen Traviss
Invincible by Troy Denning

This is a post-Return of the Jedi series from the Legends timeline. Think of it as an alternate universe from the sequel movies and newer books.