Commander Nebula is the counterpart of Nebula from the Alternate Universe, where Buzz Lightyear's counterpart is the evil emperor. He is one of a handful of Space Rangers known to have survived the destruction of their Star Command, with others including XR, Mira Nova, and eventually Booster. He later intervened to stop his team from killing the main universe's Buzz Lightyear so that they could join forces with him against their Buzz and the main universe Zurg. Having defeated the alliance of evil, Nebula and his team returned to their home universe to reclaim it, having acquired supplies from their new friends in the main universe.
Interestingly, the XR of the alternate universe refers to this Nebula as "Pop" like the original universe XR, but the alternate Nebula doesn't object to it like the main universe one does. This may be indicative of a closer relationship between the alternate universe versions.