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They first appeared in The Adventure Begins along with the Grubs, where they started torturing several LGMs before Zurg decides to torture them himself. Buzz and his partner Warp Darkmatter head off to rescue the LGMs, though Zurg and his army escape while Warp is presumably killed.
The Brain Pods appear again where they and the Grubs put off their finishing touch of new weapons for Zurg's right-hand man Agent Z, who turns out to be none other than Warp himself. Though Warp finds his new agent name to be stupid, the Brain Pods convince him to take it to avoid Zurg's wrath.
Later on, one of the Brain Pods informs Zurg that the LGMs are connected with the Uni-Mind, which is a mystical orb that enables all LGMs to feel and think as a collective whole, which is situated on their homeworld. As that point, Zurg decides to utilize the Uni-Mind by kidnapping more of the LGMs in order to take control of every innocent mind in the Galactic Alliance.
After captuing the Uni-Mind, Zurg had the Brain Pods and Grubs to work on giant ray gun that will manipulate the Uni-Mind's powers and the entire Galactic Alliance to his own will. Fortunately, Buzz uses his sense of justice and virtue to free the Uni-Mind and save the Alliance, thus leaving Zurg and his army's plans for conquest in vain.