Comparisons have been made between Dark City's villain Mr. Hand and the villain from the Matrix Trilogy, Agent Smith. Both are enforcers for the film's antagonists (the Strangers/the Machines), but both are somehow different from their otherwise homogeneous fellows. Both develop a bond with their human opponent (Hand through Murdoch's memories, Smith through Neo's code), which causes them to become more human and to develop some of humanity's worst characteristics. Subsequent movies in the Matrix Trilogy further this comparison, as the climactic fight scene in Dark City is not unlike the one seen in Revolutions.
Nor do the comparisons end there; both Matrix and Dark City concern artificial memories and habitats, and both are patrolled by faceless superpowered beings challenged when a human develops comparable powers. Comparisons have been made between scenes from the movies, making note of similarities in both cinematography and atmosphere.Template:Ref
The Animatrix short story A Detective Story is remarkably similar to Bumstead's story arc in Dark City. In the short story, a detective is pursuing an enigmatic figure (Trinity, who like Murdoch is an "enlightened" human with knowledge of the false nature of their reality). Over the course of the investigation he learns that the previous investigators went insane or disappeared. In the end, the detective catches up with his target and learns the true nature of his world, only to die shortly thereafter.
The overlying plot of the anime The Big O also features an isolated, noir-esque city, where virtually everyone suffers from amnesia, people possess memories that are not their own, and in the end it is revealed that the city is apparently some sort of experiment, ending and resetting itself every forty years.