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Fly, Arlene, Sears, and Roebuck eventually reach the home planet of the Freds, but it is completely deserted. Only a single Fred corpse is to be found, as well as one corpse of another species, an alien grey sort of creature.
The crew revives and questions both creatures, and learns that this new race is known as the "Newbies" (in broken translation of the Freds' language). Newbies have destroyed the Freds' planet and are now headed for Earth. The species evolves at an extraordinary pace, and this Newbie tries to disable the ship to avert a reunion with the rest of its kind. Following the captured Fred's instructions, the Marines arrive on an uncharted desert planet.
On this planet dwell humans, survivors of the Fred invasion. Fly and Arlene are welcomed as legendary heroes, but Fly is suspicious of the natives' strange emotional state. Eventually Fly and Arlene kidnap a human to the medical lab and examine him, and learn that the Newbies have evolved into microscopic entities which can live inside humans.
Fly discovers that faith is fatal to the Newbie microbes, and begins curing humans with sermons. Eventually, he has enough "converts" to mount an attack on the refugee ship, but the Newbies win; Fly and Arlene are captured and their minds copied into a computer simulation of Phobos.
Fly and Arlene awaken outdoors. Evading a rocket attack, they and the liberated humans flee in an escape pod from the Freds' ship. The planet's moon turns out to be a hollow spaceport. The band of survivors acquires a ship and makes haste for Earth, knowing that, at best, they will arrive a month after the Newbies do.
Four hundred years after they last saw their home planet, Fly and Arlene finally return. Signs of civilization remain on the surface, but all is awash in uncontrolled plant growth and no human beings are visible. Finally, they reach Salt Lake City, which has been rebuilt. The Newbies are nowhere to be seen.
Arlene, realizing what this means, contacts the Tabernacle. The call is answered by Jill's mind, which has been copied into yet another computer. Jill allows the ship to land and meets the Marines in the form of a hologram, who explains everything.
For the past six million years, the Klave and the Freds have been fighting a war over the interpretation of ancient texts, created yet millions of years earlier by the same race who originally built the Gates. When the Freds encountered Earth in the 1400s, they withdrew for some centuries and developed a scheme to subdue the human race by impersonating demons. During those centuries, however, humans evolved, which caught the Freds by surprise (humans and Newbies are the only known races which experience evolution). The humans fought back, and ultimately won.
Fly and Arlene are reunited with Jill, who had herself cloned and cryogenically frozen in case the war heroes should return. Albert, although he had made cryonics his career, did not live long enough to have the same opportunity; Fly and Arlene are shown a box labeled "Albert", presumably containing his ashes.
The whereabouts of the Newbies is explained by events in their computer simulation. Fly realizes that the scenario is intended to stimulate their memories of the Phobos mission, and begins changing the events, recruiting an Imp and other monsters to his cause with sermons. Eventually, a large horde of converted demons and zombies helps Fly and Arlene find a "back door" to the simulated world and escape.
The back door opens to reveal a single Newbie, in the form of a giant black slug, wired bodily into the computer program. The Newbie is dragged back into the simulation, where the accelerated passage of time intensifies its evolutionary behavior out of control, destroying it completely. Because all Newbies are telepathically linked, the entire species evolves out of existence simultaneously.
The simulated Fly and Arlene, believing their original bodies to be dead, decide to live inside the simulation for as long as it is powered. They attempt to make themselves comfortable by remembering alternate events.
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