The company left the console business in 2001 to concentrate of software development for multiple platforms. They are heavily centered around the arcade business. Sega is currently part of the Sega Sammy holding company, which also owns a variety of companies, including Underground Liberation Force or ULF Records, and TMS Entertainment aka Tokyo Movie Shinsha, an animation studio.
See the Wikipedia entry on Sega for further information about the real company.
The Black Ops is the department that employs Dom and is apparently not too concerned with the methods needed to achieve their ends. It has not been made clear in the comic how close Dom's goals align with his employer. It's possible his actions are attempts to recruit Erika and Kimiko for another Sega division. The Black Ops provided Dom with a minivan loaded with special equipment in Strip 280.