A mysterious new hacker known only as the Puppet Master threatens to create chaos, erasing and rewriting the memories of his victims: humans who have cast away their physical body to become cyborgs. Is he an evil genius, or could he signal the beginning of a new age in the relationship between man and machine?
Yes, it's glaringly obvious that both of these manga series were created by the same mangaka, but that in and of itself isn't necessarily a reason to recommend anything. Although these two series don't share the same setting or characters, many plot and design conventions are similar, i.e. cyberpunk elements, emphasis on tech and weaponry, and the occasional philosopical musing. Appleseed focuses more on combat than the cerebral meandering of Ghost in the Shell. A staple of both series is artificial intelligence, and the consequences of its application in society.
The characters in Cowboy Bebop and Ghost in Shell are relatively similar in the same good guy/bad guy fashion. Also the thematic concepts involved add to each of the plots.