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.

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.

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 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.

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.

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.

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 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 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’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 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.

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.

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 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?

Gir has recently been watching a movie he rented from the local mall, in which Zim just happens to be in the room when the FBI Warning is displayed on screen. Just as Zim realizes this, he gets a phone call from the mall saying they need the video back, in which Zim begins to panic because he believes that there is foul play at hand. When his computer tells him that the FBI must be an alien hunting group, he grabs the movie and makes his way to the mall, despite the fact that he doesn’t know what to expect when he arrives.

When Zim goes to Mars to attempt to find a way to destroy the Earth, figuring that whatever killed the life on Mars may work for Earth as well, he stumbles across the face on Mars, which he later discovers that is actually the controls for a spaceship, in which the entire planet of Mars was the spaceship. Dib learns of this and he attempts to go to NASAPLACE in order to get them to see what Zim is doing, but they refuse to believe him as they can’t look at the monitors. Will Dib be able to find a way to stop Zim before he uses the red planet to squish all the life out of the Earth?

When Zim is attempting to explain to the Almighty Tallest that the humans are both dumb and tall, he gets interrupted when the doorbell rings and his transmission to the Tallest is cut short. The two individuals at the door claim to be human, but Zim doesn’t believe them and he attempts to tell them that their spaceship is jamming his signal; they respond by merely sacking both Gir and Zim and taking them to their spaceship. Will Zim be able to get back to his base and finish his report to the Tallest, and what will Zim do to the two aliens who dared to capture him?

The Almighty tallest are examining a storage planet in order to send valuable goods to the Invaders to help them on their missions. They decide to send a Megadoomer Combat Stealth Mech to Invader Tenn to help her conquest of the planet Meekrob and they decide to send a box of malfunctioning SIR units to Invader ZIM, but when the two packages addresses are switched by an angry slave, ZIM gets the Megadoomer and plans to use his new gift from the Tallest to put an end to Dib once and for all.

An Irken masquerades as the new girl at school in order to settle an old score with Zim.

While at school one day, Zim throws another fit about the lunch food so Dib throws a muffin at him, which causes Zim to run away in anger. The next day, a pair of Meekrob come to Dib in his sleep and grant him marvelous super powers, in which Dib decides to use to put an end to Zim once and for all. When Dib manages to suppress Zim quite easily, he decides to use his power for the greater good and he lives out the wonderful life he always wanted to have; though perhaps it’s too wonderful.

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.

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.

Gaz develops an unhealthy fondness for the flavor of pork.

Zim's former boss is mad at him for leaving, so he kidnaps him and makes him work at his old job on the planet Foodcourtia.