The intergalactic adventures begin with the third season premiere episode when Bender's uncle, The Archduke of Thermstadt, dies. He leaves his gothic castle to Bender... on one condition -- Bender must spend a full night there. In a homage to classic horror movies, Bender becomes cursed and transforms every night, threatening the entire Planet Express gang.
Bender and Fry volunteer for military duty to enjoy the benefits of the soldiers's discount. When war breaks out later that same day, Leela too decides to join the all-male ranks, under the guise of Lee Lemon, and creates quite a stir for her leader, Zapp Brannigan.
When Leela accidentally leaves the keys in the ignition of the Planet Express, Fry and Bender decide that it's the perfect opportunity to go joy-riding. This decision, unfortunately costs the entire crew their jobs -- and Fry and Bender lay blame on Leela. She decides to return to her former job at the cryonic lab, but before doing so accidentally implants her job chip into Fry and his chip into her. Now Fry is in charge of assigning jobs to the recently thawed and Leela is one of the best-looking pizza delivery girls in New New York. Fry's first assignment on the job brings him a big surprise -- he unthaws Michelle, his former girlfriend from 1999, who voluntarily froze herself after Fry's disappearance.
When Fry eats an egg-salad sandwich from a vending machine at a gas station, he begins to have strange side-effects - he becomes stronger and smarter. Professor Farnsworth makes a diagnosis and concludes that Fry had ingested 'intelligent worms' that have set up shop in his body. Because these worms are so smart, the regular means of flushing them out will not work. The Planet Express crew must shrink themselves to microscopic form and enter Fry's body to fight off the intruders. Meanwhile Leela is left to divert Fry's attention, but finds herself more and more attracted to the new man Fry has become.
When Zapp Brannigan, Kif, Leela, Amy and later in a rescue attempt Bender and Fry crash onto Planet Amazonia, the crew discovers the planet in inhabited by a race of giant women who have found that life without the male gender is preferable. These Amazonian woman worship a Femcomputer who sentences Fry and the rest of the guys to death. It is up to Bender; a manbot and technically not a man, to intercede on the guys' behalf. Meanwhile, Kif professes his love to Amy.
When a sleep-walking Bender causes havoc on Planet Express by indiscriminately bending things in the middle of the night, Professor Farnsworth becomes bent out of shape and sends him off to the Bending Factory where his uncontrollable need to bend becomes controlled. There, he is re-united with Flexo and meets Anglelyne, a curvaceous fembot, and sparks begin to fly.
The Earth is conquered by flying brains with the power to turn normal human beings into idiots. On a distant planet, Leela learns that humanity's single hope is Fry - the only being immune to the brains' moron-making power. So Leela must return and enlist Fry's help without becoming an imbecile herself.
Dr. Zoidberg tries his luck as a part time comedian much to the dislike of his audience. He decides to get professional help - his old uncle formerly famous Harold Zoid. Zoid sees no comedy talent lurking within Zoidberg though and decides to go with drama. They get AMC actor Calculon to do a main role by promising him an Oscar.
The Professor decides to ship hazardous cargo to the outer reaches of space, but the course chartered takes the ship through some environmentally sensitive areas-- including the penguin refuge on Pluto. Leela refuses to transport the dangerous cargo, so the professor removes her from command and installs Bender as captain. While Bender is piloting the ship, he allows his attention to drift and accidentally showers the penguins with oily goop.
After a string of bad luck, Fry remembers back to when he was growing up in New York and his older brother, Yancy, was stealing his good ideas - until the discovery of a rare seven-leaf clover that reversed Fry's luck. Now in the year 3001, Fry sets out in hopes of regaining his luckier days by recovering the charm from the underground ruins of Old New York and the family homestead. But strong-minded Fry becomes incensed with his unexpected discoveries.
When Leela rushes to the reunion of the Orphanarium where she grew up, she reunites with Adlai, a plastic surgeon who can give her the appearance of two eyes. With terrible childhood memories of her strange Cyclops look fresh in mind, Leela is convinced to undergo the surgery, while Adlai is convinced that Leela is the only one for him. Meanwhile, Bender petitions to adopt 12 orphans in order to receive a government stipend for which he has big plans. Daddy Bender and Leela see things in a new light.
When Fry and Bender are mistaken as bank robbers, they are sentenced to time in an insane asylum for robots. Bender, of course, sees it as a vacation, but Fry begins to crack under the pressure of mechanical examinations and a diet consisting of motor oil. Fry soon becomes convinced that he too is a robot and is declared cured and released back to New New York. Bender and his new partner in crime, Roberto, escape from the asylum and attempt to rob a bank only to find the cops waiting to bust them. On the lam, the seek refuge on the Planet Express and take the crew hostage.
Bender no longer lives up to his name after an unfortunate accident, but instead makes a new name for himself when rock star Beck offers him an opportunity to live out his folk-rock dream. As a result, Bender's attempt to showcase his humanistic endeavors fails when he's faced with a bittersweet realization. Meanwhile, the rest of the crew gets a taste of the '60s.
In the 30th Century, the once entertaining Harlem Globetrotters are now feared as they will humiliate any planet in the Universe who dares to play them. Feeling up to the challenge, Professor Farnsworth creates a group of mutant basketball players to go head-to-head with the Globetrotters. Farnsworth's secret winning ingredient is chronitons, time particles found in the Tempus Nebula. However, when the Planet Express crew removes the mutants from harvesting, they tip of the Time/Space Continuum causing forward motion of time to skip ahead.
Fry falls in love with Liubot (guest star Lucy Liu, 'Ally McBeal'), a virtual humanoid downloaded from a computer. Disapproving of Fry's affair with a virtual woman, Bender and Leela steal the original head of Lucy Liu from the internet company, Nappster.com, where she is being held against her will. Seeking revenge, the Nappsters unleash a mob of illegal Lucy Liu downloads to take over the city.