Sebastian is first seen in a cage at Rob's lab. After Ratso makes a rude comment about the other animals and is unmoved by the fact that Rob (the Master) has returned, Sebastian points out that Ratso does care about the Master, even though he's too proud to admit it.
Sebastian is later present during the "Remember That Day" sequence but is unable to recall the time when the Master first found him. Later, the monkey tells Toaster and the others about how he had been abused by humans, which is why his arm was in a bandage. When Kirby refuses to believe Sebastian's story, the monkey asks him if he wants proof, and Kirby insists that a little proof would be nice. Sebastian then removes the bandage on his arm to reveal his (invisible) scar to Kirby and the others, and Kirby tearfully apologizes. When Blanky asks Sebastian if it hurt, the monkey replies in agreement.
Sometime later, Sebastian asks to be helped out of his cage so he can do some computer research and recover the Master's lost thesis, which he needs to graduate college. As Sebastian approaches the computer, Radio pointlessly broadcasts the event. Sebastian then begins typing on the computer, which soon comes to life and gives the monkey some handy computer advice during the "Super Highway" sequence.
When Sebastian resumes typing on the computer, the monitor suddenly becomes infected by a virus, prompting Toaster and the gang to pull the plug before the computer explodes. Sebastian then whimpers because he saw something on the computer screen before it was shut off. The other animals then learn that Mack plans to ship them to Tartarus Laboratories to be used as test subjects. Mack later walks into the lab and teases Sebastian by offering the monkey a potato chip. When Sebastian reaches for the chip, Mack tricks him and calls him a "stupid monkey" for always falling for that one.
Ratso later leads Toaster and company to a recent disturbance that was coming from the basement. However, Mack shows up shortly after and prepares to ship the animals, but is stopped by Kirby (who was unable to fit inside the vent and was then given the duty to protect the animals). Sebastian watches with delight as Kirby chases Mack around the lab, but the latter eventually manages to lock Kirby in a closet.
When Sebastian and the other animals are eventually shipped by Mack, Toaster and the gang chase down the truck. When they manage to catch up with the truck, Ratso asks if everyone is okay, and Sebastian replies, "Luck and a blanket was with me this time."
Sebastian is last seen in his new habitat at the zoo during the "Hang in There, Kid" sequence and playing checkers with a fellow ape. He also appears briefly on Wittgenstein's computer screen with all the other protagonists of the film.