Dedicated Irken soldier Zim is sent on a secret mission to Earth, where he disguises himself as an elementary-school student and gathers information about human beings. His plan is moving smoothly until an extraterrestrial-obsessed classmate named Dib takes notice of Zim's green skin and missing ears.

When Zim makes a huge scene over his inability to eat lunch food, he overhears one of the girls at school talking about how inhuman he seems to be and how he has no friends. In an attempt to appear more normal, Zim decides to spend time with a student named Keef, though Zim soon finishes his plan and he considers himself normal, so he tries to get Keef to leave him alone. Much to Zim’s chagrin, however, Keef continues to follow Zim around, so Zim decides to take unorthodox measures to ensure Keef leaves him alone.

Zim attempts to test some of the defenses that Earth has by taking his Voot out for a drive to monitor local police units. However, when a bumble bee crashes into his vehicle, Zim comes crashing down in the park, in which he heads home because he will be unable to recover it the next day. However, when a space cult known as the Saucer Morons discover the Voot first, Zim must find a way to get his vehicle back without causing him to lose his cover.

When Zim’s Voot Cruiser has a mechanical failure and it sends Zim and Gir flying through the skies, Zim manages to gain control just in time to land safely in their headquarters. However, Zim is highly upset because a human baby saw the whole thing and despite Gir’s attempts to reason with him, Zim decides to go meet with the baby to see what he can do. However, Zim soon discovers the true nature of the baby and he must do everything he can to prevent them from accomplishing their goals.

Dib believes he has figured out a way to successfully tunnel into Zim’s underground base, but when his father comes in and announces that it’s the Membrane family’s night out and that Gaz gets to pick the place to eat, Dib runs off saying that he will be back in time for them to leave. However, when Dib fails to arrive on time, Professor Membrane decides to wait until Dib gets back, which causes Gaz to become quite frustrated as she really wanted to get some of her favorite food; she decides to go find Dib at Zim’s place and despite the fact that Zim’s already taken Dib into an in-space laboratory, she refuses to miss her opportunity to eat out so she plans to let nothing get in her way.

After another day at the Earth skool, Ms. Bitters reminds the children that it’s Parent Teacher Night and that all the parents must come to the skool at the end of the day. Zim becomes worried because his robotic parents aren’t programmed for such a task yet and he cannot permit them to blow his cover, so he attempts to help them become the parents they should be, but Gir’s carefree nature soon puts his plans in jeopardy.

When it begins to rain one day, Zim becomes worried because he’s never experienced rain before. Dib takes notice of his fear and he coaxes Zim into stepping into the rain, only to discover that the Irken race has an innate weakness to water, which causes a burning sensation upon impact. Dib decides to exploit this new fact to create the ultimate weapon to stop Zim once and for all, but Zim himself attempts to find a way to protect himself from this new found weakness, which all leads up to a confrontation that neither of them would have expected.

While at skool one day, Ms. Bitters tells the class that they need a new pet hamster due to the orders of the skool’s board of directors. When the hamster arrives, all the children love the hamster because of how adorable it is, in which Zim decides to exploit that fact since the hamster could help make the humans too weak to resist him. Zim plants an Irken device on the hamster that will permit it to grow larger and be controlled by Zim, but when the hamster grows rampant and breaks free, Zim must attempt to stop the huge hamster from destroying his headquarters, all the while worrying about the growing military presence that may have no choice but to attack the hamster, which would ruin all of his efforts.

Zim's Yuletide plan to overtake Earth by posing as Santa starts to backfire when he takes on characteristics of the Jolly Old Elf. Dib, meanwhile, tries to save the population from impending doom.

Zim goes on an outing to the downtown area in order to test a new guidance chip he installed in GIR, but when GIR removes the chip before leaving in order to store a cupcake, Zim and GIR are left lost and have to resort to public transport to find their way back. Their journey home is complicated further by Zim temporarily losing his vision by looking at the sun, his disguise being mistaken for that of a bank robber, and his escape from the police being wrecked by GIR replacing his extra rocket fuel with tuna fish.

When Dib finally manages to be permitted to present his findings on Zim to the Swollen Eyeball Network, he believes he will be able to put an end to Zim’s schemes once and for all. However, when he discovers that he needs his father’s permission and since his father is busy working on his television show, Dib must venture into the studio where his father is in order to attempt to get the signature he needs; though he soon discovers that speaking to his father isn’t going to be as easy as it should be.

When Dib once again notices that Zim isn’t eating his food, he throws a piece of bologna at him in order to taunt him, in which the bologna fuses with Zim’s skin, causing him immense pain. Zim vows to get his revenge and during the next day of school, Dib sits on a tack, which causes Zim to begin laughing hysterically. Dib believes Zim is just being pathetic, but when Dib begins to transform into a living piece of bologna, he realizes that Zim’s plan was better than he had thought and he must formulate a method of curing himself before it’s too late.

When Dib discovers that Tak’s ship he recovered has a built in AI, he decides to reprogram the ship with his own personality. While Dib is quite pleased with initial results, the spaceship begins to behave more and more like the real Dib and it attempts to actually take his place. All of the attention of a huge spaceship going to school causes Zim to realize that it’s really Tak’s ship, so he plans to override the machines AI and order it to attack Dib; though can he really force a machine so smart to attack it’s counterpart?

Dib talks to a counselor about his belief that Zim is an alien.

When Dib finally manages to get a picture of Zim without him in his disguise, Zim formulates a plan to shrink himself down into a microscopic size to get into Dib’s body and perform a brain wipe to prevent him from remembering where he located the picture. Fortunately for Dib, his father has been working on some technology that may just help Dib stop Zim before it’s too late, though he’ll been to be careful because he’s extremely vulnerable due to the fact that Zim is inside of him.

When Zim’s headquarters are having security problems, Zim attempts to upgrade the security system and get the job over with. He decides to put Gir in charge of ensuring nothing goes wrong while he replaces the computer’s AI, but when Gir begins to mess around with things, he inadvertently causes the house to shut down along with himself. However, Zim soon discovers that Gir’s AI has been uploaded into the central hub of the house, which worries Zim quite a lot since Gir is being unresponsive and uncontrollable, which soon puts their mission in jeopardy.

Zim finally finishes one of his self proclaimed brilliant inventions, a space-time-object-transfer device, in which he plans to send a giant robot into the past in order to put an end to Dib once and for all. However, when the robot isn’t compatible with the temporal field, he throws a rubber pig into the vortex instead, which turns out to be compatible and it causes Dib to crash his tricycle in the past. Zim decides to send many more rubber pigs into Dib’s past, which ultimately affect him in the future; though when Zim overdoes himself, he discovers that history isn’t something that should be messed with.

Dib interferes majorly with Zim's plan to bring the Almighty Tallest to Earth just as he's preparing to bring about the downfall of the human race with mind-sucking parasites.

When Dib finds out that Zim has no human organs, he attempts to exploit Zim’s ailment of head pigeons to get the skool’s nurse to examine Zim in hopes she will see the truth. However, when Dib blurts his plan out to Zim, Zim develops a device that will permit him to switch objects for organs, in which he begins to steal the organs of his fellow classmates in order to appear more human in time for his appointment at the nurse’s office.

When Zim formulates a plan to get revenge on his skoolmates and especially Dib, he gets them all participating on a fieldtrip. Dib, however, realizes that the driver of the bus isn’t real, but due to his constant theories, the other students disregard his warnings. Zim decides to gloat about his magnificent plan and he informs Dib of every detail in confidence that Dib can do nothing to stop him, though Dib refuses to give up and he does everything he can to save his skoolmates and himself; despite the fact that he doesn’t know why Zim’s plans involve a room with a moose.

Dib summons Mortos der Soulstealer, a mystical being who emerges once every thousand years, in order to wish for him to steal ZIM’s soul. However, when it turns out that Mortos needs to recharge his power before he can complete the task that Dib requested, Dib must help him do many absurd things in hopes of putting an end to ZIM once and for all. Meanwhile, ZIM heads around town undergoing his latest evil scheme, which is the reason Dib was so eager to enlist Mortos’ help in the first place.

When Zim comes home from a lousy day at skool because he found out that Dib knows a flaw in his security system, Gir attempts to cheer him up by rubbing bacon oil all over his face. However, when Zim develops a pimple due to the grease, he fears that he will be considered abnormal and that it will jeopardize his mission. Zim believe he can use some acne medicine to get rid of the pimple, but when it only gets worse and when Gir draws a little face on the pimple, Zim believes all hope is lost; though Zim soon discovers the pimple has hypnotic powers and he hopes to exploit this new power in order to get Dib to reveal his secret.

When Dib finally manages to get a spy camera inside Zim’s house, he plans to exploit the moment to show the Swollen Eyeball Network the truth about Zim’s nature. Unfortunately for Dib, Zim is more concerned with Gir’s waffles than his next evil plan, which causes Dib some complications as there is nothing special about waffles. However, when something out of the ordinary does occur, Dib believes he may just have a chance to succeed in his plans.

After Zim watches an old movie where some invading aliens are defeated by some bacteria, he begins to study germs more. However, when he discovers that such germs truthfully are everywhere, he begins a crusade to kill every germ in his headquarters so that he can be safe, which is helped by the fact that Gir had some cleaning spray handy in the house; though when the cleaning bottle runes dry, Zim must attempt to go to the store and get some more, despite the fact that he knows just how many germs are out there.

Ms. Bitters is assigning students their mentors for Career Day through the use of an aptitude test and a machine. Both Dim and Zim attempt to get their desired professions on the test, in which Dib manages to get paired with a Paranormal Investigator while Zim gets stuck working at a fast food facility. However, when Zim misinterprets the 8 billion served sign and thinks that the individuals in charge of the company are the leaders of the planet, he becomes dedicated to his job in hopes of being promoted to Lord of All Humans. However, thanks to the alignment of the planets, Zim is about to go through some uncontrollable changes that could jeopardize his mission; which Dib is looking to exploit, though both Zim and Dib find their situations to go much different than they anticipated.