Nefarious's office was located in many of Nefarious's bases including his Deep Sea Hideout and the Nefarious Space Station.
Ratchet & Clank: Up Your Arsenal
Nefarious's office at his Deep Sea Hideout contained his Secret Agent Clank Holo Vision collection and a datadisk of Tyhrranosis's defenses. Ratchet and Clank infiltrated the hideout and located his office and found an encrypted Star Map which Al was later able to decode.
Ratchet and Clank Future: A Crack in Time
Nefarious's office at the Nefarious Space Station had a desk, a bed, a couch and a holo-vision.
Notes and references