The series begins with Logan being captured and prepared for the adamantium bonding process. There are several mentions of his being tough, and the Professor, the director of the Weapon X program, along with his assistants Dr. Cornelius and Miss Hines, wipe his mind and bond adamantium, the hardest known substance on Earth, to his bones to prepare him to be a mindless, soulless killing machine. Prior to Wolverine volume 2, #75, the plot had too much adamantium bonded to his forearms for an unknown reason, resulting in his claws, leading to the installation of silicon sheathes around the claws to prevent sepsis and silicon bushings through which the claws emerged from his body, and surgical alterations to connect his musculature and nervous system to the claws to provide sensation and control.
Throughout the program, Logan is constantly referred to not as a person but as a subject, and his humanity is almost completely disregarded in the course of the experiments. Logan frequently comes to odds with his mental programming, and eventually escapes into the wilderness after killing all of the soldiers there (except for one, future Weapon X Director Malcom Colcord) while the Professor, Cornelius, and Hines lock themselves in a secured room that Logan cannot break into.
Psychologist Suzana E. Flores has interpreted the storyline as a narrative of the psychology of torture, including the perspective of the victim and the perpetrator of torture, particularly as practiced historically by states, now recognized as a crime against humanity. She argues that the story illustrates Martha Nussbaum's understanding of objectification, including aspects of instrumentality, denial of autonomy, inertness, fungibility, violability, ownership, and denial of subjectivity. Flores particularly compares the behavior of the scientists in the story with the medical professionals of Nazi Germany. Flores also draws the studies of obedience and complicity in torture by Stanley Milgram and Philip Zimbardo.[2]
Issue 48 of Wolverine's first ongoing series has a cover plugging itself as "The sequel to Weapon X". The issue involves Wolverine making preliminary investigations into his past, and included remakes of three scenes from the Weapon X story. It is collected in Wolverine Visionaries: Marc Silvestri, among other Wolverine stories from the era.
Suzana E. Flores, The Psychology of Marvel's Wolverine, McFarland & Co, 2018, p. 35-50.