Jacob knows Motoko's been looking for a new body, so when he responds to the alert about a break-in at Wayne Enterprises and sees her deeply-uncanny new body lying like a lifeless mannequin on an equipment table, he's able to put two and two together without too much trouble.

The would-be thieves, however, do not know the full story. They just know there's valuable technology around for the stealing. And guess how valuable Motoko's disconnected brain casing looks right now?

Answer: Valuable enough that Jacob punches out a guy in a stereotypical black woolen cap who is reaching for it. As the burglar hits the floor, Jacob snatches the brain up and tucks it under his arm like a football as he runs, looking for a safe place. The Major is his friend, and he's not going to let her get sold on the black market by these jackasses.