To do that, he wants to lure the worm into a trap and then attack it from behind, for which he needs access to an Elder spacetime conduit. The crew raid an alien museum owned by the Wurgalan, a client species of the Bosphuraq, but the conduit they acquire is broken. They go to another location where the Thuranin are lying in wait after they discovered what the Dutchman was after and sent ships to where there was another one.
They narrowly escape, but the enemy continues to close in. Skippy is still Skippy the Meh and unable to utilize any of his "Skippy Magic" as he is operating at a reduced state. At the last minute, Joe has the idea to plot a jump point through an Elder wormhole. This temporarily breaks the Elder wormhole, destroys the Thuranin ships guarding it, and will further confound those looking for a mystery ship with advanced capabilities.
With no other options available, they go to the "Roach Motel", a star system where ships enter but do not leave, hence the name. It is protected by a stealth field that disguises what is inside, a powerful damping field that prevents any ship from jumping out, and Guardians: powerful AI ships built by Elders to guard the system.
The Guardians shear the Dutchman in half when they enter as part of their protocol. Skippy is able to get them to stop, but the damage is already done. The Dutchman no longer has engines with which to propel itself or reactors to sustain critical functions. They abandon what is left of their ship for a nearby planet they name Gingerbread, which they get to using the dropships onboard the Dutchman. With the Dutchman in ruins and the existential threat to humanity, the plan is to make Gingerbread a new home for humans.
Skippy discovers that there is a gas giant in the system that has been stealthed by the Elders. He can tell due to its gravitational effect on the other planets in the system and that its mass causes the star to wobble. They name it Vera.
They encounter non-cyborg Thuranin on the planet, the descendants of those who had made an expedition into this area centuries prior and also had their starship destroyed. They shoot down a Dragon dropship Joe is on and he crashes into a lake, sinking to the bottom. The water pressure is so high that he can't get the door open to get out. Skippy saves him using missiles to drain the lake into an underground aquifer, but it isn't enough. Joe is saved at the last minute by using the nanocord in the ejection mechanism to burn through the door to get to the surface, where he was extracted to safety by balloons.
With some difficulty, the SpecOps teams find and retrieve the Elder conduit Skippy needs to kill the worm in an underground facility, but it is also broken. Joe doesn't give up on the Dutchman and takes off into space to salvage parts from all the wrecked ships that were destroyed by the Guardians.
They scavenge bits and pieces here and there in a shuttle, but they don't add up to a ship and Skippy is still dying. Eventually, Skippy finds a dead Sentinel in the system, which is highly unusual. Hans Chotek is convinced by Staff Sergeant Margaret Adams to let them investigate the wreck for an Elder conduit after initially refusing to give them permission.The Guardians are concerned with how close the Condor dropship is getting to the Sentinel and demand that they stop. Joe has the idea to fling himself and Skippy over to the ship as they will be a lower threat profile than their dropship. It works and they find the conduit they are looking for, but Skippy needs the power from Joe's suit to jump start it. Joe himself goes offline for a bit, but all is well in the end.
Skippy kills the worm and the Merry Band of Pirates rebuild the Dutchman with him out of salvaged parts.
When they are done and are ready to depart, an ancient Maxolhx ship comes to life and is intent on destroying them. It was lying in wait for a long time and became aware that there was a ship moving around the system that was not being destroyed by the Guardians. The Maxolhx have evidence that the Dutchman's crew are humans as they were communicating on their zPhones without any Skippy encryption, although these Maxolhx are so old they don't know what humans are, but they are broadcasting in the clear, message containing sensor data of the Dutchman with video of Joe talking into a zPhone.
Using missiles, microwormholes and Joe's ingenuity, Skippy projected a big hologram behind the Maxolhx ship through the tiny far end of the microwormhole. Skippy also fed hard radiation through the microwormhole, bleeding charged particles off our main reactor. Finally, he created spacetime ripples that were weak and harmless, except that to the Maxolhx, they appeared to be the beginning of the vicious spacetime sheering effect that had torn apart the Dutchman. And a long time ago, they had torn apart the Maxolhx ship.
They are able to scare the Maxolhx ship off. It decides to get the hell out of dodge, which is a problem as it will transmit the data about the humans once the Maxolhx ship is outside the system. The cobbled-together space bus that is the Dutchman can't catch them, nor can it jump ahead as both ships are in a damping field. Normally the Guardians would obliterate them, but Skippy told them not to when they first entered. He can't specify what they do other than to turn them ON or OFF. Unleashing the Guardians would mean the Dutchman would be destroyed as well. That's something the Dutchman's crew consider as a last resort.
Using more missiles and microwormholes they are able to precisely pinpoint the location of the stealth Maxolhx. When they do, a jump wormhole is formed inside the Maxolhx ship using a jump drive that is outside of the Dutchman. As a result of the damping field, the wormhole explodes, taking the Maxolhx ship with it.
One of the Maxolhx survives in an escape pod and is brought on board. Joe nicknames the Maxolhx, "Mr. Snuggles". Chotek attempts to negotiate with him. It doesn't go well, with the Maxolhx being dismissive of humanity and promising to kill every human in the species. He uses his nanobots to attempt to free himself and take control of the ship. He fails and kills himself in despair.
The Dutchman leaves the Roach Motel with it being impossible that the Guardians would let them back in again. There was more to explore in that star system, but they will never get the chance.
While the Dutchman was in the Roach Motel, the Maxolhx outside the system had been seriously disturbed by the Dutchman's damaging of an Elder wormhole. The Maxolhx decide to investigate other wormholes that have been manipulated by this mystery ship, starting with the Gateway wormhole that was closed at Earth.