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 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 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.

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 attempts to taint the Earth’s cow-meat supply with sewer water is ruined because of Gir’s antics, he decides to increase the power on Gir’s behavioral modifier, which will permit him to stay in serious mode all the time. However, when the serious Gir starts to consider Zim a threat to the mission and runs off to learn things on his own accord, it’s up to Zim and Squidman to find Gir and turn down the power on his behavioral modifier before too many individuals see them and jeopardize their mission.

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.

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.