See also: Eras of Play
5 to 37 Years after A New Hope
In this Era The New Republic is in place, although a small Imperial Remnant maintains control of a portion of the galaxy. The Jedi, on the rise again thanks to the efforts of Luke Skywalker, are at a crossroads. Some members of The Order, which numbers about one hundred individuals, want to take a more direct and deliberate role in galactic affairs. Skywalker, meanwhile, is struggling with whether or not he wants to reestablish the Jedi Council. Rash Jedi have led New Republic officials to be wary of the Knights, and suspicious of their true motives. Indeed, this leads to varying degrees of mistrust and even fear in the general populace, many of whom still remember the Emperor's anti-Jedi rhetoric from years before.
The first galaxy-wide threat in The New Jedi Order Era is the Yuuzhan Vong invasion. It begins with Nom Anor, a spy who sows additional seeds of discord throughout the galaxy. His efforts give rise to antitechnology cults dedicated to the destruction of innocent Droids. Masking his true identity, he recruits agents from native populations to carry out acts of sabotage and subversion. Nom Anor, however, is only the beginning of the Yuuzhan Vong threat.
The Yuuzhan Vong are humanoids that follow a religion of pain and nature. They hate machines of all kinds, using instead living technology that they have bioengineered to serve as ships, weapons, tools, and tools. These fierce, holy warriors seek to conquer the galaxy and bring their faith to the infidels who regularly make use of unclean machines. Their invasion begins on far-flung worlds such as Belkadan and Helska, but they quickly widen their hold on key sectors of the Outer Rim and Mid Rim, terraforming worlds to produce the yorik coral and other living materials that serve as their ships and weapons. The Jedi learn, to their horror, that this intractable new enemy cannot be sensed through The Force. The Jedi, former guardians of peace, become the hunted prey of the Yuuzhan Vong. Meanwhile, the extragalactic intruders continue their relentless advance toward The Core, crushing any force that dares stand in their way. A few worlds surrender without a fight, while those that resist are rendered uninhabitable. In time Coruscant itself falls, signalling the death of The New Republic.
Eventually the Yuuzhan Vong discover their history may not be as they thought, when the living planet Zonama Sekot came to Coruscant and fought defensively against the Yuuzhan Vong, "Welcoming home it's true inhabitants." The new Galactic Federation of Free Alliances (Galactic Alliance) allows the Yuuzhan Vong to surrender and take Zonama Sekot as their homeworld. While not all Yuuzhan Vong accept this, the primary threat of the Yuuzhan Vong ends as Zonama Sekot flies into Hyperspace to seek a new home for the Yuuzhan Vong in The Unknown Regions.
Though the war is over, many threats still exist. Some Yuuzhan Vong and their cults still fight against technological civilization. The Galactic Alliance has to rebuild the galaxy. And The New Jedi Order seeks out threats to peace and justice.