As so often happens in the G.I. Joe series, the Baroness gets caught in the crossfire between Cobra Commander and Destro. In these issues she and Destro attempt to make a getaway, but she fails to board the helicopter in time. Destro wants to go back for her, but Billy knocks him out so they can escape.
An unconscious Baroness is then taken captive by Cobra Commander, who brings her to his hideout aboard the Arbco Valdez. The Baroness wakes up while in flight, complaining about the fact that she is guarded by mere 'low-ranking morons'. Cobra Commander knocks her out once more with a classic uppercut, after which she is restrained in one of Cobra's infamous Brain-wave Scanners.
Source: Digital copy of the comic