Most of Albert's dilemma begins with his wife, Jennifer West, who has a slight variant of Alzheimer's disease. Although most Alzheimer's patients can receive ultrasound therapy to mitigate its effects, Jennifer's particular case would require constant therapy, which could be just as harmful as the actual disease. Due to this, Albert theorizes about using nanobots to manually eliminate the plaque that causes Alzheimer's; however, because he would require living subjects in order to get accurate results, he is not able to research the nanobots on Earth. This is when Jeff Murray gives Albert access to MPO, where research laws are not nearly as strict.
While Albert is researching, a co-worker, Murdoch Rascowicz, is keeping an eye on the research to steal and sell it for his own profit. At some point, the nanobots begin to behave erratically, destroying tissue in the subject and repairing it just for busywork. Albert tries to tone down this behavior, but Rascowicz prefers this direction for the nanobots and decides to intervene. Rascowicz initially plans to kill Albert through an "accident", but it fails; the accident befalls a different person. However, Albert is framed for this person's death and thrown into the MPO Prison. At this point, the intro to Subterrain begins.