Two years after Galactor's defeat and Condor Joe's apparent death, Leader X attacks a cruise ship, killing nearly everyone aboard. One survivor, a young girl, is captured by X and rapidly aged into the bizarre, masculine-voiced villainess Gel Sadra. Despite her adult appearance, Gel Sadra frequently throws childish tantrums and behaves immaturely.
As Galactor revives, the Science Ninja Team is called back into action, with a shady man named Hawk Getz acting as Joe's replacement. Getz is quickly revealed to be a disguised Galactor agent who killed the real Getz, and he is slain by a mysterious feather shuriken. After hints dropped in the first three episodes, Joe reappears in the fourth episode, having somehow survived his fatal injuries from the original series, and rejoins the team. It is later revealed that an ex-Galactor scientist rescued him on the brink of death and gave him various cybernetic augmentations.
Later in the series, a female scientist named Dr. Pandora is introduced, having lost her husband and daughter in the cruise ship disaster. Unbeknownst to her, her daughter Sammie survived and is actually Gel Sadra.