Zim finds that he is severely allergic to the school cafeteria's food, and Dib uses this fact to try to prove to the other children that Zim is an alien. Zim escapes and uses a listening device planted on the back of Dib's head to spy on Dib's house—Zim discovers that Dib intends to kill him with the cafeteria food. Zim and Dib stage an apocalyptic food fight in the school cafeteria, which ends with Zim escaping and Dib being blamed for the food fight.

The Irken race is having a great assigning for Operation Impending Doom II, where all Invaders are assigned a planet to conquer. Wanting to rid themselves of the irritating and arrogant Zim, the Almighty Tallest give him a faulty SIR unit (named GIR) and send him to the farthest reaches of space. When Zim arrives, he finds a planet named Earth where he sets up base and, in disguise as a human, infiltrates the local school. Unfortunately, one schoolmate, Dib, is a young paranormal investigator, who vows to capture Zim and prove that he is an alien.

Zim notices that all the other children in the school have friends except him. Zim conducts a series of bizarre tests on some students in order to select the "best" friend. However, it proves harder to lose a friend afterward than it was to gain one.

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After Dib sneaks into Zim's base and takes incriminating pictures of Zim without his disguise on, Zim shrinks to microscopic size, enters Dib's body, and manipulates him into destroying the storage disk with the photos on it. However, when Dib reveals he has a copy of the disk hidden in his house, Zim travels to Dib's brain to erase the memory of where the copy is hidden.

Parent-Teacher Night is approaching and Zim is confronted with the fact that he doesn't have any parents. He makes use of his robot parents to attempt to fool the students, teachers, and parents, despite knowing that they are not equipped for such a job.

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Zim goes on an outing to the downtown area 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 being temporarily blinded after looking at the sun, his disguise being mistaken for a bank robber, and his escape from the police being wrecked by GIR replacing his extra rocket fuel with tuna fish.

Zim sees a B-movie where advanced extraterrestrial life is thwarted by common germs. Zim becomes acutely germophobic and dedicates himself to studying and exterminating all of the Earth's bacteria. After running out of germ spray, he heads out to buy more, but GIR runs off to a "MacMeatie's" restaurant. There Zim discovers that he can protect himself from germs using a germ-resistant hamburger "meat" made of recycled napkins, which is sold there.

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When a pigeon lands on Zim's head in class, he is sent to the nurse's office for having "head pigeons", but becomes concerned that the nurse may discover that he is not actually human. To avoid this, Zim steals human organs from other children.

Note: Dark Harvest (and the series in general) became controversial when it was mentioned at Scott Dyleski's murder trial in 2006.^[20][21][22]

Zim's spaceship is sent spiraling out of control after an encounter with a bee and crash-lands in a park. Zim attempts to recover it, but a meeting of UFO enthusiasts finds Zim's ship. Zim is captured by the group once his disguise falls apart, and they begin worshipping as their prophesied alien god. Eventually, Zim gets in contact with GIR who is able to rescue him and recover the spaceship, but a second encounter with a bee causes the duo to crash-land at a much larger UFO convention.

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Dib discovers that water is harmful to Zim. After Dib splashes Zim with a puddle and a water balloon, Zim vows to wet Dib as a form of retribution.

It's career day at school and Dib has been paired with a paranormal investigator named Bill while Zim goes to work at MacMeatie's. However, after discovering Zim is moulting due to "the galactic equinox", Dib tries to convince his new mentor to help him expose Zim.

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Dib desires to do a presentation about Zim for a meeting of the Swollen Eyeballs, a secret society focused on the paranormal. Before he can do this, the society requires that he must have a permission slip signed by his father, Professor Membrane. Professor Membrane is very famous, so he has a television show and Dib must endure various trials to gain access to his father.

Zim discovers that the planet is being stolen by "planet jackers", aliens who use planets as fuel for their dying sun. After failing to persuade them to leave the planet for his conquest, Zim attempts to steal the planet back.

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Zim is outraged when he discovers that Dib knows of a flaw in his base's defenses. He also develops a hypnotic zit after GIR covers his face in pizza grease, which he uses to gain control of the schoolchildren and force Dib into revealing the weakness in his base. At that point, the pimple grows to monstrous proportions and explodes; Zim then leaves to reinforce his base, while Dib is forced to clean up the mess.

During maintenance of Zim's underground base, GIR's brain is accidentally put into the house's operating system.

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Using a time portal device, Zim hopes to go back in time and kill Dib's younger self. However, he discovers that he cannot send himself through time and instead decides to send rubber pig toys into the past in an attempt to injure Dib. After some initial success, Zim realizes that altering the past can cause undesirable results in the present.

Zim orchestrates a fake field trip for his schoolmates, intending to send them to an alternate dimension that consists entirely of a room occupied by a moose.

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Zim's class at school gets a new hamster and Zim decides that its cuteness can be used as a form of mind control. Zim attaches a device to the hamster which turns it into a colossal, superpowered, Godzilla-like monster. Unable to control it, Zim instead allows the hamster to rampage throughout the city. But when the hamster heads for Zim's base, Zim is forced to team up with Dib to stop it.

Zim fears that he has been seen out of disguise by a human baby. Believing the baby to be a threat to his mission, he attempts to interrogate it. He soon after finds out that they are in fact aliens that have been stranded on Earth.

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It's Gaz's turn to choose a restaurant for the family's annual night out. When Dib fails to return from an attempt at defeating Zim, Gaz sets out to rescue him and return in time to make it to the restaurant.

The school starts a candy fundraiser, which Zim is initially not interested in, until he finds out about a secret prize.

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Zim gets scared after finding an "FBI Warning" on a rented film that GIR keeps watching. Zim takes the DVD back to the mall to return the disc and avoid the wrath of the FBI.

Dib throws bologna at Zim during the lunch break at school, which dissolves his skin. As revenge, Zim places a thumbtack on Dib's chair, which Dib sits on. The next day, Zim informs Dib that he infected Dib with a virus that is altering his DNA, turning him into bologna. In revenge, Dib also infects Zim with the virus, forcing both to team up in an attempt to find a cure.

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Gaz is in line for a newly released handheld games console when the person behind her tricks the salesperson into giving the final console to him. Gaz will stop at nothing to obtain the Game Slave from the boy.

Zim sends out probes to the planet Mars to see if the planet is of any use for the Irken Empire. When the probes send back photos of artificial-looking structures, Zim and GIR travel to Mars only to discover that the planet is actually a giant spaceship. Zim then plans to pilot Mars to Earth and kill all life on it. Dib discovers Zim's plan and gains control of Mercury, which is also a spaceship, in order to stop Zim's plan.

Dib accidentally creates a portal in his own forehead which leads to a dimension filled with monsters. Dib passes back and forth to the dimension and forces Zim to come through with him. The monsters capture Zim and say they won't release him if Dib doesn't allow them access through the portal to Earth. However, when the monsters look through the portal, they turn back as they are disgusted by the sight of GIR eating candy.

Dib goes on his favorite TV show, Mysterious Mysteries, to tell the world the story of Zim and to share a video of Zim he had filmed. To Dib's surprise, Zim, GIR, and Gaz also appear on the show to tell their sides of the story. They each tell their own versions, which are then performed in reconstructions on the show for the benefit of the viewer.

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Professor Membrane constructs an energy-creating device, and Zim gets the idea to sabotage it to destroy the world.

Zim requests more powerful weapons but the Almighty Tallest do not want to give them to him, so he is sent to the deadly training planet Hobo 13 to prove his worth. Zim, through extreme selfishness and sacrifice of his teammates, surprisingly gets to the end of the trials.

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Zim is doing time-related experiments on Dib, but the experiment explodes. Dib manages to escape but he is "slowed down" and can only move very slowly. Also produced is an explosion, which is also exploding very slowly.

Zim is accidentally shipped a high-powered robot mecha with a cloaking device and immediately heads off to destroy Dib with it. The robot does not come with batteries, requiring the machine to be plugged into a power outlet to stay cloaked. Unbeknown to Zim, only the robot is able to become invisible, with himself and the power cable being plainly visible the entire time.

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There is an infestation of head lice at the school and so an extreme lice hunter comes to investigate the outbreak.

Zim and GIR are abducted by two aliens who think of them as human and dog specimens.

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Frustrated at how people see paranormal science, Dib sets out to disprove the legend of Chickenfoot, who is actually a man stuck inside a chicken costume.

Zim is frustrated with how useless GIR is, and puts him in a hyper-competent "Duty Mode". However, the new GIR sees Zim himself as a threat to their mission on Earth.

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Zim is hit by a muffin during the school lunch break and suspects it is Dib who threw it, but he cannot know for sure. That night, in a dream, Dib is visited by aliens who say they have given him special powers. Dib then uses these powers to threaten Zim, who willingly turns himself up and has GIR self-destruct. Time passes and Dib spends his life solving other mysteries and thwarting aliens. Finally, at a very old age, Dib is interviewed on TV and admits to having thrown the muffin. At that point it is revealed that Zim had simulated Dib's entire life just to find out whether or not Dib was the one who actually threw the muffin.

An Irken, Tak, joins Zim's class in disguise as part of a plan to hollow out the Earth's core and prove herself worthy of being an Invader. Zim, Dib, Gaz, and GIR team up to stop her. At the end, Dib laments that he is unable to explore beyond Earth, only for Tak's abandoned ship to crash right in front of him.

Zim desires to bring his leaders, the Almighty Tallest, to Earth to witness his next plan for world domination involving a brain-eating parasite, so he remotely takes control of the "Massive". However, at the time he takes control, the Tallest are under attack from an anti-Irken resistance group known as "The Resisty". Meanwhile, Dib has been attempting to salvage/reverse engineer Tak's spaceship (which he acquired in "Tak: The Hideous New Girl") and manages to repair enough of its systems to establish a remote connection, get into Zim's computer, and wrestle for control of the Tallest's ship. When the Tallest realize what is going on, they transfer their hacked power-core to the Resisty so their ship is pulled toward Earth, forcing them to evacuate and destroy the ship to protect the secrets of its technology. The Tallest then contact Zim to punish him for what he has done, only to find that he is under attack from the brain-eating parasite.

Dib summons a mystical ghostly beast called Mortos der Soulstealer to attack Zim and prevent him from taking over the world. Mortos will grant Dib anything he wants, but is tired and requests time and food to regenerate. It soon becomes clear that Mortos just wants to have fun, and spends time eating and trying on clothes. Dib confronts Zim with Mortos and demands that he fulfill his request to stop Zim, but Mortos grants a random person's request for ice cream instead and returns to his realm to rest.

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Dib has managed to get a spy camera into Zim's base in the hopes of recording some evidence that will prove he's an alien. Unfortunately for Dib, his hard drives aren't working and need to be automatically repaired, so Dib watches Zim while this is happening. It is a quiet day for Zim. GIR is trying to get Zim to eat waffles, but every now and then he reveals part of an evil plan or gets attacked by a giant flesh-eating squid. Every time this happens Dib tries to contact a member of the Swollen Eyeball to witness it, but by the time they answer Zim is eating waffles again, and he eventually throws up on Dib's camera. Dib's hard drives finally repair, but then the cyborgs sent by Zim destroy them.

A girl selling cookies gets her foot trapped in Zim's front yard, attracting nationwide attention. The girl loves all the attention and won't let anyone simply pull her out. Dib manages to persuade the president to use a digging machine to dig under the girl to get her out, which will expose Zim's base in the process. Zim finally decides that enough is enough and simply pulls the girl out of the hole.

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Dib is again working on Tak's crashed spaceship, which turned on him the last time he activated it because its computer AI is a digital copy of Tak's mind. To stop it from acting so hostile to him he downloads his own personality into the ship. This does not go as planned because the ship then starts to believe that it is Dib. Zim discovers what Dib has done and reminds the ship that it is Irken technology and must do what Zim says. Zim commands the ship to throw Dib into the city sewage plant but the ship remembers that it is Dib, and throws Zim across town. The ship is so depressed that it is "Dib" that it deletes its personality.

Dib sees school counselor Mr. Dwicky about his problems and tells him about how Zim's an alien trying to take over the Earth. Surprisingly Mr. Dwicky says he believes him and that he wants to help him out. He later reveals to a colleague that this is just a ruse to get Dib to trust him. They trick Zim into thinking aliens are coming to meet him in the woods to give him super weapons but after a while of waiting, Mr. Dwicky reveals he doesn't really believe Dib. At that point, some real aliens turn up and offer to take Mr. Dwicky with them. As he loved aliens as a child he jumps at the chance and Dib is left behind with nobody else believing him.

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Zim decides to use the school's election to gain power, so Dib becomes the manager of his opponent to try and stop him. Zim streaks ahead after making many promises to the students that are crazy but wins them over anyway. Dib counters this by using a cellphone to feed dialogue to a boy who is opposing Zim so he can debate with him properly. Dib's candidate wins the election, but the school faculty brings him to a lab where they remove his individuality and free will, making him nothing more than a mindless figurehead. Needless to say, Dib is not pleased, as Zim would have met this fate if not for his efforts.

Dib discovers that his electronic spell drives still have two credits on them, which allow him to cast spells. Not knowing what the spells would do, he casts one on his sister Gaz instead to see what would happen, causing everything she eats to taste like pork. To help Gaz, Dib decides to go to another dimension to request the spell be undone. Gaz must face the Shadowhog and answers three questions correctly to reverse the spell. As part of a deal he imposed on the creator of the spell, Dib is stuck cleaning toilets with brushes on his head.

Zim is abducted by his former boss, Irken Frylord Sizz-Lorr, and forced to resume his previous job working in a fast food restaurant on the Irken-controlled planet of Foodcourtia. He then must escape before a massive amount of snacking causes the planet's gravity to prevent anyone from leaving for 20 years.

Zim discovers how much people like Santa Claus and decides to use this in a plan to take over the world by dressing up in a Santa suit full of data about Christmas. The Santa suit malfunctions and engulfs Zim, effectively turning him into a real Santa Claus before Dib beats it and then launches it into space. The episode ends two million years in the future in which it is revealed that the Santa suit (now massive) returns to Earth every Christmas to wreak havoc and eat milk and cookies.

When Zim suddenly reappears to begin Phase 2 of his evil alien plan to conquer Earth, his longtime nemesis Dib sets out to unmask him once and for all.