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.

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 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 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.

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’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.

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.

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?

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.

During Probing Day, the day where the Tallest evaluate the Invaders’ performances, Zim has Dib captured in a space-time-field prison which is keeping him in slow motion, in which Zim wants to perform experiments on him for the Tallest. However, when a malfunction causes the prison to explode, Zim finds a piece of explosion that is expanding very slowly; in which Zim believes he can end if he throws it into the city’s cesspool. However, when he discovers that getting the explosion to the cesspool is much more difficult than he expected, he finds that he may just have to use unconventional means to complete the task.

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.

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

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.