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.

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.

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.

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.

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.

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.

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.

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.

Zim is upset because all of the other Invaders are doing much better in their tasks than he is, though he inadvertently discovers that his signal to the data hub has been interrupted. When Zim takes a closer look, he discovers that the Earth has actually been hijacked by the Planet-Jackers, an alien race who must throw other planets into their dying sun in order to survive. Zim begins to formulate a plan to stop the Planet-Jackers, but when Dib refuses to believe him, he realizes that he must save the world he plans to destroy by himself, just for the sake of being the one who gets to destroy it.

When Gaz sees an advertisement for the new handheld gaming console, the Game Slave 2, she decides that she really needs to go to the mall in order to get one. However, when her father insists that she takes Dib to the mall as well, he forces her to wait until Mysterious Mysteries goes off, which causes them to arrive at the mall late. Gaz, in rage, tricks Dib into running off into the underground parking lot while she attempts to get a Game Slave 2; though Gaz discovers an annoying kid managed to get the last copy so she seeks to steal his copy, all the while Dib must attempt to get out of the underground parking lot, which is filled with rat-like people who just annoy him.

It’s Halloween and the entire town is getting into the Halloween spirit; much to Zim’s dismay because he considers the entire concept to be insane and he doesn’t want filthy Earth children coming to his house. Meanwhile, Ms. Bitters sends Dib to an insane asylum because he has been acting crazier than normal, in which in truth he has been getting sucked into a nightmare world that was created due to his meddling with one of his father’s inventions. After finally getting out of the nightmare world and out of the insane asylum, Dib sees Zim’s house and decides to force Zim to come with him into the Nightmare world because he believes Zim will have the capability to put an end to all the madness, but will they manage to work together despite the fact that they’re enemies and that Zim didn’t want to help him in the first place?

When Mysterious Mysteries is having trouble in ratings due to their lack of stories, they decide to take drastic measures and they finally let Dib onto the show. Dib believes this is his best chance to reveal Zim for what he is and he plays a short clip of Zim and Dib in the woods, which actually makes the anchor of the series quite pleased. However, when Zim gets on the show the next day to attempt to prove Dib wrong, they soon get into a battle of words over the real events that occurred on that day as they both attempt to persuade the host of Mysterious Mysteries to believe what they have said.

Professor Membrane has just unveiled a world changing machine that will completely remove the entire need for fuel, though if the machine were to malfunction, it could cause a giant shockwave that would destroy all life on Earth. However, Professor Membrane refuses to turn the machine on until his children are present, in which Dib is absent because he is attempting to prevent Zim from sabotaging the machine. However, things soon take a turn for the worse as Dib falls into one of Zim’s traps and the crowd in front of Professor Membrane beings to grow uneasy over the fact that they’ve waited so long, so Professor Membrane decides to send Gaz to go find Dib and put an end to his foolishness.

The skool is holding a candy drive in order to get some finances, in which the individual who sells the most chocolate bars will get a secret mystery prize. Zim becomes interested and he attempts to find a way to sell the most chocolate bars, which causes Dib to get into the contest in order to gain a defeat over Zim. Zim soon realizes, however, that he may have to take drastic measures in order to sell more candy bars than Dib.