After the royal council approves his idea (assuming that Flik would not be around to cause any more trouble), Flik leaves Ant Island and ventures to the city (rubbish under a caravan), where he mistakes a recently fired circus troupe for warriors when some of them do an act based on Robin Hood. After Flik returns to Ant Island with the circus troupe, he introduces the ants to the troupe, but the troupe refuses to believe the reason Flik has recruited them and fly across the stream from the Ant Island, with Flik in pursuit. After a nearly fatal encounter with a bird in which Dot, Atta's little sister, is saved by the circus bugs, Flik is given the privilege to speak with Atta herself, in which Atta apologizes to Flik for her misjudgement.
Learning from Atta that Hopper is afraid of birds, Flik comes up with an idea and tell the circus bugs that they will build a makeshift bird, controlled from the inside, to scare Hopper away, as long as they keep the idea secret from the rest of the colony. The idea goes into motion and, during the process, Flik is shown acting awkwardly around Atta and staring lovingly at her. After the bird is complete, the ants celebrate and Atta thanks Flik for finding the "warrior bugs," getting their antennas tangled. But when the circus troupe's leader, P.T. Flea, arrives at the island in search for them, Flik's mistake is made public to the colony. An upset Atta sees Flik through his lies and regrettably has him banished, this time for good. Downhearted, Flik leaves Ant Island with the circus troupe.
However, Dot catches up with him, and tells him that Hopper, who invaded the island with his grasshoppers, will kill her mother, the Queen, after they have finished gathering food. The circus bugs suggest using the false bird, but Flik says it won't work, much to their shock, and acknowledges that the colony was right to kick him out for being such a screw-up and doesn't want to do anything, believing they will be better off without him, but when Dot brings him a rock and uses his words from the beginning from the film, Flik feels better and is motivated to return to Ant Island, where he, Dot, and the Blueberries climb aboard the "bird" and take control the model. The plan almost works, but the "bird" misdirects and crashes into the circus wagon, freeing P.T., who sees the "bird" and sets it on fire, prompting Flik to crash-land the "bird."
Hopper, realizing that he has been tricked, hires his henchman Thumper to savagely torture Flik when Flik confesses that he is responsible for the mayhem. Despite the injuries he has sustained, in the film's turning point, Flik redeems himself by standing up to Hopper, exposes his plot to kill the Queen, and states how ants are not meant to serve grasshoppers, but are awesome creatures who are strong in number. Flik's speech astonishes every ant in the colony, including Princess Atta. Infuriated by Flik's defiance, Hopper attempts to squish Flik, but Atta rushes in to stop him, tells him to leave, and helps Flik up, commending him for his bravery.
Inspired by Flik's speech, the ants and the circus bugs take a stand against Hopper's gang and scare the grasshoppers away. Flik and the other ants seize Hopper and shove him into the circus cannon, but the rain falls, prompting the ants to run for it, but Flik is still injured and collapses while running. As Atta rushes over to help Flik up, a humiliated and vengeful Hopper then pops out of the cannon and takes Flik hostage as he flies away. The circus bugs attempts to give chase, but are unable to do so as they end up being stuck in a tree. However, Flik is rescued by Atta, whom he instructs her to take him across the stream to the other side where he has previously encountered the bird. As Atta watches worriedly, Flik faces Hopper, who backs him to the bird's nest and chokes him. As the bird picks up Hopper in its beak, Atta quickly pulls Flik to safety, and they cringe as the bird lowers Hopper into the beaks of its chicks.
When spring comes, the circus bugs prepare to leave, and P.T. Flea asks Flik if he is sure he can't come on a tour with them, to which Flik answers that he belongs to the island, as well as with Atta, who has since made up with him. The circus bugs thank Flik and, along with the ants, applaud at him for his heroism and intelligence. Atta then approaches Flik and kisses him, choosing him as her mate. Flik then rushes over to help Heimlich, who has emerged out of a cocoon, still a caterpillar, but now with small butterfly wings, into the air. As Flik waves good-bye to his friends, he is taken to a tree root by Dot and Atta for a better view.