After escaping to the moon, Gwen obsesses over the now ancient Lunar Revolt (as described in The Moon Is a Harsh Mistress) and Mike (Mycroft), the self-aware computer responsible for the uprising's victory. Gwen claims to have been present during the revolt, and despite her claim that she was only a girl at the time, the math still doesn't add up, and Campbell grows suspicious.
Still pursued by unknown assassins, Campbell and Novak are rescued by an organization (later revealed to be called the Time Corps) under the leadership of Lazarus Long. After fitting Campbell with a new leg (he had lost the bottom half of one of his legs in combat years before), the Time Corps attempts to recruit Campbell for a special mission. Accepting only on Gwen's account (Campbell's new bride is revealed to have been a member of the Corps from the beginning), Campbell agrees to assist a team to retrieve the decommissioned supercomputer, Mike. Engaged in frequent time-travel, the Time Corps has been responsible for changing various events in the past, creating an alternate universe with every time-line they disrupt. Mike's assistance is needed in order to accurately predict the conditions and following events in each of the new universes created. Campbell's frequent would-be assassins are revealed to be members of contemporary agencies also engaged in time manipulation who, for unknown reasons, do not want to see Mike rescued by the Time Corps.
During the mission (which is only mentioned briefly at the end of the story), Gwen is grievously wounded and Campbell loses his foot again, though the Time Corps is successful in retrieving Mike. The story ends with Campbell talking into a recorder (presumably the source of the first-person medium through which the story is told) reflecting on the mission and his relationship with Gwen.
The Cat Who Walks Through Walls may be regarded as part of Heinlein's multiverse series, or as a sequel to both The Number of the Beast and The Moon Is a Harsh Mistress. During a meeting of the Council of the Time Scouts, representatives from every major time line and setting written by Heinlein appear, including Glory Road and Starship Troopers. Additionally, the Council has a sitting member from the Lensmen written by E.E. Smith.
The title of the book refers to a cat by the name of Pixel, who has an inexplicable tendency to be wherever the narrator happens to be (see Schrödinger's cat). However, Pixel is only a supporting character who doesn't appear in the story until the final third of the book.