Endgame: A Novel (Doom #4) (1996) (edit title/settings)

(taken from wikipedia)
Traveling on the captured Fred ship towards the alien's homeworld, Fly attempts to while away the time on the 2 month/200 year journey while dealing with Arlene, who is depressed about not being able to see Albert again, and Sears and Roebuck, who are convinced that they are locked on a suicide mission. Eventually, Fly rallies the group to begin training and preparing for defensive action following the landing on the Fred's homeworld, planning to take as many of the Freds with them as possible.

Arriving on "Fredworld", the quartet find the planet deserted. They learn from reanimating a Fred body that the planet was invaded by the "Newbies", a new race of aliens that learn and evolve at a rapid rate. The marines find a Newbie, who leads them to a planet 120 light years from the Fred homeworld. During the voyage, the captured Newbie attempts to change the ship's course, expending all the braking fuel before he is killed by Fly. Sears and Roebuck are forced to decelerate the 3.7 km ship via friction and air-breaking in the planet's atmosphere, during which the stresses on the ship, assisted by a hit from a weapon on the surface, destroy the vessel as it crashes into the planet.

The quartet survive the crash and seek out the weapon, discovering humans. They are captured and taken to a human starship, where Fly and Arlene learn that the war is over, although humanity has become a communistic race, exhibiting extreme amounts of social atomism and an extreme fear of death. The marines discover that the Newbies are infecting the humans, existing at the same level as DNA. Fly figures out that a human with faith in something cannot be "infected", and stages a rebellion on the ship. The rebellion is defeated, Sears and Roebuck are killed, and Fly and Arlene have their souls (or copies of their souls) placed in a computer simulation of Phobos and Deimos.

In the simulation, Fly figures out that the programming is influenced by his memories; by lying to himself, he is able to alter what happened. He collects a force of imps, zombies, and other demons on his quest for Arlene, and they later find a Newbie soul in the program, which, aided by the mind-directed simulation, evolves out of existence. A trapped Fly and Arlene decide they will attempt to remember the invasion as an outright defeat for the Freds, creating a Utopia for themselves; if this works is not revealed in the books. This makeshift army eventually entraps the 'essence' of one of their adversaries, a 'Newbie'. This essence evolves fairly quickly into a form unconcerned with basic reality.

Outside the ship, Fly and Arlene wake up. The "soul-sucking" computer cannot remove human souls completely. Along with their faithful (the humans worshiping Fly) and the bodies of Sears and Roebuck, they escape incineration by the launching human starship. They travel to the destroyed remains of the Fred ship that took them to the planet in the first place, and find an intact and working med-lab. Using this lab, they figure out that it works using symbols. Finding a symbol that looks as close to the Klave as they can, they shove Sears (or Roebuck, they don't know which) into a drawer-like part of the lab and activate the machine, reviving the body of Sears or Roebuck, who then revives his counterpart. After Sears and Roebuck is revived, they find an intact escape pod that was not destroyed in the wreck and use it to get into the orbit of the planet, and take another ship from the planet's artificial moon. They chase after the Newbie-human ship, which is heading for Earth, although on arrival, they discover that the Newbies never arrived, likely having evolved out of existence as well (as affected by the Newbie soul the game-force had captured).

Landing at a rebuilt Salt Lake City (which was destroyed by nuclear weapons in the third novel), Fly and Arlene head to the Tabernacle to find out what happened to Jill and Albert. The pair encounter an AI, and nude clone of Jill, and a black box with a glowing orange light simply labeled as "Albert", which presumably contains his consciousness (Fly and Arlene discover that Albert spent many years researching a way to extend the human lifespan so that he would be able to see Arlene again). Arlene is visibly overwhelmed by the realization of this, and the book series abruptly ends on this note.