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.

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 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.

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.

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.

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.

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.

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?

When at skool one day, a child comes into class late because his head was itchy, which Ms. Bitters recognizes that it was due to lice. Before she can do anything, however, the lice infect the rest of the students in the class, so Ms, Bitters informs the Delouser, who proclaims martial law and the children are taken into separate rooms. However, Zim shows no sign of being infected by the lice, which causes the Delouser to take special interest in him.

When a girl named Moofy comes to Zim’s house and attempts to sell him cookies, he freaks out and sends a robot gopher to get rid of her. However, when Moofy falls into a hole, the story breaks out and a crowd of people and a news agency shows up to cover the breaking events. Zim is worried because he doesn’t want his identity to be revealed, though he begins to formulate a method to exploit the moment to free Moofy and help him destroy the world.