Unknown to its creators, the Jarts were able to open a gate into the Way, where they settled and spread for three hundred years before the descendants of the Stone's original human occupants evacuated the Stone and moved along the Way. Their first encounter with the Jarts resulted in a major war that ended in a stalemate, and in the second half of the book it is revealed that the Jarts are on the verge of breaking through the Hexamon's defenses. In the novel's final climax, the Jarts launch an all-out offensive to destroy the Hexamon by opening a gate directly into the heart of a star, allowing superheated plasma to enter and blast along the Way, destroying everything in its path.
To counter the threat, a coalition of the Geshel faction and "liberal" Naderites seizes control of the Nexus and launches a daring but highly risky plan to save the Hexamon culture and destroy the Jarts who occupy the Way. They take over both Axis City and the Stone, and after evacuating the Stone for safety, they give the Hexamon's inhabitants and the 21st century humans a choice between two means of escape— either fleeing back up the Way in two of the self-contained Axis habitats, Axis Nader and Central City (which can travel along the Way's central singularity), or staying in the "present day" solar system, with the Stone and the other two Axis habitats, Axis Thoreau and Axis Euclid.
The first part of their plan involves hitching Axis Nader and Central City units to the tube-like singularity that runs through the center of the Way, and accelerating them to near light-speed. The Hexamon scientists theorize that the time-space shockwave generated by their massive acceleration will act as a sort of "battering ram", protecting them from the oncoming blast of stellar plasma, while simultaneously sealing all the open gates along the Way and destroying all the occupying Jarts. The other half of the plan requires the separation of the Stone and the Way— after triggering massive explosive charges to blow the cap off the end of the asteroid and sever the junction between them, they reactivate the Stone's engines to steer it clear of the Way, and eject Axis Euclid and Axis Thoreau out into 'normal' space, where they will join the Stone in permanent Earth orbit, after which the open end of the Way will seal itself, closing off access between it and the 21st-century Earth timeline — although the possibility remains that the machinery in the Stone's sixth chamber could be used to reconnect the Stone and the Way in the future.
Meanwhile, the "old Earth" humans in Axis City must also make their escape. The rescue party sent to find Vasquez returns to the end of the Way aboard their V/STOL - hitched to a new "tuberider", they must race ahead of the coming destruction to reach the rapidly closing aperture of the Way. But Vasquez hopes to find a way to return to "her" Earth timeline, before the Death. During her internment with the Hexamon, she has been taught the technique of opening new gates out of the Way, and she has been given a "clavicle", an advanced Hexamon device that allows her to locate and open these trans-dimensional portals. With the star plasma rushing towards her position, Vasquez frantically searches through the complex enfolding space-time geometry in the wall of the Way, and with only moments to spare she passes through in a protective capsule— only to find that she has chosen the wrong gate and has landed in an alternate Earth timeline.