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The General Lee was acquired for the War Pigs in order to make them mobile. An old ship, it was retrofitted by pilot Nuura Joss over the course of three weeks. During that time, she developed an emotional connection with the ship and became defensive over any negative comments directed at it's age.
The War Pigs were assembled for a secret mission—find the Hephaestus, which was carrying secret Megamedes Project data, recover it, and kill everyone on the battlecruiser. Upon meeting with the rest of the War Pigs at the ship, Joss asked them what they thought of it. Iggins, a mechanical genius, was especially dismissive of it, prompting Joss to threaten to "put [him] down" if he put the ship down again. The Lee carried out its mission successfully.
In 2502, after the War Pigs reunited, the General Lee took part in a mission at Moria and suffered a coolant leak, making warp travel hazardous. Nuura Joss suggested taking the ship to the Apollo Shipyard at Grissom IV for repairs, but the team (except Romy Pyrius) were captured by the Screaming Skulls, a mercenary and smuggler band. The pirates boarded the vessel, but were killed by a stim-abusing Pyrius, who then turned the ship's weapons on the station. Technicians who had been captured by the pirates were put to work repairing the General Lee. Meanwhile Pyrius stole a xel'naga crystal from the pirates, and this "malign alien force from beyond the grave" exposed the darkest parts of the psyches of the War Pigs, triggering various forms of malaise, strange behaviors and insanity. A trio of Dark Templar boarded the ship, retrieving the crystal.
After tracking fugitive Jim Raynor to the world of Urona Sigma, the General Lee touched down on the world to release most of the War Pigs onto the planet. However, after it reentered orbit, it came under attack by Cerberus Program commander Lars Trakken's Wraith.
Trakken and his heavies later boarded the vessel in an attempt to find and kill Nuura Joss, but she was able to elude the resocialized troops and escape in an escape pod. She was sad to abandon the vessel and vowed to retake it.
The War Pigs ended up stranded with Jim Raynor on the surface of Urona Sigma when the protoss began a purification operation. However, Lars Trakken descended with a squad of Cerberus troopers in a dropship in order to personally oversee Hickson's death. Raynor and the War Pigs ambushed the troopers, stealing the dropship and returning to the General Lee.
The ship may be named after the The General Lee, the signature automobile from the television series The Dukes of Hazzard, which was in turn named for Confederate general Robert E. Lee. It was partly inspired by the Millennium Falcon of Star Wars.