A double-date for Kif, Amy, Zapp, and Leela ends in disaster when their orbiting restaurant crashes on planet Amazonia. The hulking female inhabitants of the planet take their male captives to the omniscient Femputer, who orders Fry, Zapp, and Kif to death by "snu-snu" (sex).

When Fry becomes infested with parasitic worms that make him stronger and smarter, he finally finds the perfect way to profess his feelings to Leela. Meanwhile, the rest of the crew goes on a Fantastic Voyage-esque journey into Fry's body to eradicate the worms.

A Planet Express mission to Robot Santa's colony on Neptune leaves the murderous robot trapped in the frozen sea, and Bender takes over as Santa, vowing to bring peace and goodwill to Xmas again. But when Bender is mistaken for the real Robot Santa, he is arrested and sentenced to death.

After suffering a string of bad luck, Fry searches the ancient ruins of Old New York for his beloved lucky clover...only to conclude that his older brother stole not only his clover – but his life.

A sober Bender crashes a dark matter tanker on Pluto, threatening the penguin reserve nearby. Leela helps out in the cleanup, but when the penguins begin mating out of control, drastic action must be taken to thin the herd. Meanwhile, Bender loses his memory and becomes a penguin.

Bender's urge to bend prompts Professor Farnsworth to send him to work as a scab in a steel factory during a labor strike, where he falls in love with a shapely fem-bot named Angleyne (voiced by Jan Hooks). But Bender's old rival Flexo and the intrusion of the Robot Mafia threaten to throw a wrench into the proceedings.

Earth is invaded by super-intelligent flying brains, who sap the Earth's populace of their intelligence. Leela is taken to Nibbler's home planet Eternium, where the Nibblonians explain that only one human is immune to the brains' powers – Fry.

Dr. Zoidberg reunites with his uncle, silent hologram star Harold Zoid, and the two of them set out to make a movie together. They cast the temperamental Calculon in the lead role, who demands an Oscar for his performance, but the movie doesn't go over well with audiences. Meanwhile, Fry and Leela get stuck in the Planet Express ship as it sinks into a tar pit on the night of the movie's premiere.

Leela meets up with her former orphanarium playmate Adlai Atkins, now a plastic surgeon, who agrees to grant Leela surgery that will give her two eyes. Meanwhile, Bender adopts twelve orphans in order to collect $1200 in government stipends.

When Amy's parents' ranch is hit by a dust storm that blows away their herd of buggalo (oversized ladybugs that are treated like and have the characteristics of cattle and buffalo), Kif sets out to prove his masculinity by rounding up the herd, only to become entangled with the native Martians.

Fry and Bender are sentenced to time in an insane asylum for robots after Bender's old, psychotic criminal friend, Roberto, frames them for bank robbery. When Roberto ropes Bender into escaping the asylum and robbing the bank again, Fry actually goes insane and believes he's a robot after the asylum staff dismisses his claims that he's human and the Planet Express crew refuses to help him due to political pressure from the governor.

Farnsworth's clone Cubert teams up with Hermes' son Dwight to launch a newspaper delivery business. Farnsworth and Hermes scoff at the kids' efforts – until the delivery boys accumulate enough capital to buy out Planet Express. Meanwhile, Fry and Leela use Bender to brew their own homemade beer and treat the brewing as if Bender is a pregnant mother.

When Bender is paralyzed in a tragic can opener accident, he discovers his musical washboard skills and goes on tour as a member of Beck's folk-rock band, acting as a voice for broken robots everywhere. Fry, Leela, Amy, and Zoidberg tag along in Fry's antique 1960s VW Van.

While creating a team of mutants to play the Harlem Globetrotters, the Professor accidentally causes a disruption in time that threatens the existence of the universe. Meanwhile, Fry tries to win an unreceptive Leela's heart.

Fry discovers the ability to download any celebrity onto a blank robot, and chooses to download Lucy Liu, with whom he falls madly in love. Repulsed by this disgusting display of human/robot love, Leela, Bender, and Zoidberg set out to shut down Nappster.com and put an end to illegal celebrity downloads forever.

Leela endeavors to become the first female blernsball player, but her lack of depth perception hinders her skills. Nevertheless, she becomes the pitcher for the New New York Mets, purely for her novelty value.

Bender fears that nobody will remember him after he dies, and sees his chance for immortality when the crew visits Osiris 4, a planet with a civilization similar to Ancient Egypt, and he poses as the planet's new pharaoh.

The Planet Express crew ask three more questions for the What-If Machine: Bender asks what if he were human; Fry asks what if life were more like a video game; and Leela asks what if she found her true home.
I, Meatbag – Farnsworth uses his latest invention to turn Bender into a human for the Nobel Committee. Bender goes on a week-long eating binge that turns him into a thousand-pound, morbidly obese blob and dies shortly after inspiring the committee to become party animals like he had.
Raiders of the Lost Arcade – Earth is invaded by a race of aliens from Nintendu 64 in a manner similar to Space Invaders. Fry fails to stop the Nintendian invasion, but when their demands are revealed to be quarters for laundry, a compromise is reached allowing the Nintendians to mix their laundry with the Earthlings' in exchange for the Earth's safety.
Wizzin' – Instead of seeing what would happen if she found her true home, Leela is knocked unconscious by the What-If Machine's lever and dreams herself in a parody of The Wizard of Oz with herself as Dorothy, Fry as the Scarecrow, Bender as the Tin Man, Zoidberg as the Cowardly Lion, Farnsworth as the Wizard, and Mom as the Wicked Witch. Leela decides she wants to become the new Wicked Witch instead of going home, but her reign of terror and her dream are cut short when Zoidberg splashes and melts her with water.

Fry puts a metal popcorn pan in the microwave while a supernova occurs nearby, causing the radiation of both to rip open a time portal that sends the Planet Express crew back in time to Roswell, New Mexico in the year 1947. Bender's body is broken to pieces during the crash and Zoidberg is found by the U.S. military among the debris, and both are taken to Area 51 for experimentation. The crew requires another microwave to return to the 31st century, so they try to retrieve one without altering history. Meanwhile, Fry meets his grandfather Enos and begins fearing that he will cease to exist if his grandfather is killed. While trying to save him, however, Fry accidentally brings about Enos' death when he takes him to a house which turns out to be in the middle of a nuclear testing range. However, Fry continues to exist due to either Enos getting Fry's grandmother pregnant before dying, or was an unrelated man whose surname happened to be "Fry". He ends up having sex with his grandmother. Since Fry has already changed history, the rest of the crew decides to launch an attack on Area 51, retrieving Bender, Zoidberg, and a microwave by force and allowing them to return through the closing time portal back to the 31st century.

Bender is accidentally shot out of the ship's torpedo tube and becomes lost in space. Floating through the ethereal darkness, Bender becomes inhabited with tiny alien life forms, but has trouble playing God to their unyielding prayers.

With Planet Express in financial trouble, Fry nominates a flashy businessman from the 1980s to replace Professor Farnsworth as CEO of the company. That Guy goes on to sell Planet Express to Mom's Friendly Robot Corporation, putting everyone out of a job.

Bender receives culinary lessons from the great chef Helmut Spargle, and puts his skills to the test on national television when he competes against Elzar on "Iron Cook". Meanwhile, Dr. Zoidberg accidentally destroys Professor Farnsworth's ship-in-a-bottle and pins the deed on Fry, only to be struck with remorse afterwards.