On a diplomatic mission to the planetAndor, CaptainPicard and the crew of the Enterprise bear witness to the rank devastation resulting from the Borg invasion. With the reproductive issues that have long plagued the Andorianpeople reaching crisis level, avenues of research that at first held great promise have proven largely unhelpful, and may well indeed be worsening the problem.
Despite the Federation's seeming inability to provide assistance and growing doubt over its commitment to a staunch, longtime ally, Andorian scientists now offer renewed hope for a solution. However, many segments of Andorian society are protesting this controversial new approach, and more radical sects are beginning to make their displeasure known by any means available. In response, PresidentNanietta Bacco has sent the Enterprise crew and a team of diplomats and scientists to Andor to convene a summit, in the hope of demonstrating that the Federation's pledge to helping Andor is sincere.
But the Typhon Pact is watching, and their interests may very well lead the Andorian people down an even more treacherous path…
The Enterprise is ordered to Andor to help out with a conference that has been convened to discuss the Andorian reproductive issues. Many are worried that the research into genetic engineering will cause the Andorians to lose their cultural identity and this fear has, in some cases, led to a strong anti-Federation feeling and the belief that all non-Andorians should be expelled from the planet. At the far end of this argument are the Treishya, whose activities are bordering on terrorism.
The Enterprise crew attempt to render assistance to the Andorians but a solar energy plant their engineers had helped repair is attacked and nearly destroyed by the Treishya and an archeological party led by Picard is ambushed. During the conference, a full-scale riot takes place and, although Starfleet manage to bring things under control, there are a small number of deaths. Matters are made worse when a Tholian ship visits the planet to reveal they have anonymously provided the leading Andorian genetics researcher, Professor zh'Thiin, with information they gleamed from the Shedai, information that the Federation also possessed but had classified, which increases the anti-Federation feeling.
The Treishya make their move by taking control of the Enterprise, using a device implanted by a visitor to the ship, and also storming the Starfleet compound after disabling the defences. In both cases, the engineering team are able to overcome the problem and the Treishya present are overpowered and captured, although the organisation's leader, Eklanir th'Gahryn, escapes.
However, the Andorian government chooses to initiate a vote of no confidence against their pro-Federation presider and a referendum shows that a significant but not overwhelming majority of Andorians wish to secede from the Federation. The Andorians resign their Federation membership and make approaches to the Tholians to assist with their research.
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Paths of Disharmony directly references the events of the Star Trek: Vanguard novel series with much of the storyline focusing on the ramifications of what was discovered in the Taurus Reach.
According to dialogue, one year has passed between the events of this novel and its predecessor Losing the Peace, which spanned March to May 2381. This contradicts references within the book to Picard's son being slightly over a year old, since the child was conceived in December 2380 according to Greater Than the Sum and would have thus been born in September 2381.
This storyline features the Andorian civilization terminating their membership pact with the United Federation of Planets.
The novel shares several similarities with the proposed Star Trek: Deep Space Nine storyline involving planet Vulcan leaving the Federation during the Dominion War; however, this may be coincidence.