Originally, in order for Zim to be assigned a planet, the Tallest would have teleported him to an Irken battle arena to fight a monster resembling a dinosaur in armour called the Digestor. This was cut for time.
Impending Doom 1
Zim's rampage across Irk was longer, with the robotic assault walker breakdancing while firing lasers, but was cut for time.
Originally, the milk carton in Dib's fridge was going to have a picture of a little girl with the words Find Me! under it. Nickelodeon didn't like this idea, so it was changed to the Rob Hummel is Meat message.
Our First Chase
Dib's pursuit of Zim through the downtown area was originally longer, but was cut for time.
Burritos Don't Like Me!
When GIR was watching TV, the word diarrhea was supposed to be brown, in reference to the color of feces. Nickelodeon didn't allow this, so it was changed to a dark red.
The cartoons GIR was watching were supposed to be old 40's cartoons, which included smoking, drinking, and gun shooting. Nickelodeon didn't allow it, however.
Originally, the ending had the taxi going to Mexico, with a sign saying Welcome to Mexico. The joke was to express just how easily Zim can get lost. Nickelodeon claimed it was offensive to Mexicans, so it was changed to something that was even more offensive that the network was okay with: CARNE, which translates into MEAT.
You Don't Like Waffles?
In the original ending of this episode, Keef would have fallen off the roof and onto a power line, where he would get electrocuted. Nickelodeon saw this as an imitatable behavior and demanded it changed. Another idea was that Keef gets run over by a car, and spins around the tire as it drove away. Nickelodeon also didn’t approve of this idea.
Zim's initiation ceremony was originally going to be shown, but was cut for time.
Originally, after Gaz accidentally drops her pizza, a rat was supposed to walk to the pizza, roll on it and walk away, but it was cut for time and the rat was changed to roaches.
Originally, Zim was going to hypnotize two other kids. The first would have been forced to eat anti-matter, and the other would have been commanded to pinch Ms. Bitters (and heard getting slapped off-screen). Cut for time.
Originally, it was going to show Zim and GIR getting their snacks in the beginning, and flying into a Poop billboard. Cut for time.
Rugrats Copyright Infringement
Tommy from Rugrats was originally going to be one of the baby-lookalike aliens. Due to legality issues, this had to be cut.
Iggins was intended to die at the end, but Nickelodeon didn't allow it. So, in the ZIM staff's tradition of mocking the network, Iggins flies from the wreckage with super-human strength accompanied by a short guitar riff.
The children in the home where Zim first uses his virtual reality goggles were originally going to be eating cockroaches until they were changed to weenies. The roaches can still be seen scuttling around the paneling, however.
The Virtual Reality scene was originally going to involve the Irken Armada reducing New York area into ruins, with the Statue of Liberty halfway under the ocean but it was changed after the 9/11 attacks. However, on this episode's first airing, it aired uncut.
Jhonen Vasquez has stated that he likes the new scene better, as he disliked the idea of having a real life city in the Invader Zim universe.
Credits of Doom
The credits of Intestines of War were originally suggested to be sexually explicit. Cut for obvious reasons.
The wreck of the car during the panic scene was originally a flaming wreck.
During the retelling sequence, PEG was going to explode and form a mushroom cloud.
Victory Over the Hogulus
Zim was going to be able to lift the boulder and hit the Hogulus, only to have the unconscious beast fall on Skoodge.
Skoodge was going to have to eat his own skin to survive, but even the production crew found this too disturbing.
Zim's exploration of the ship was originally longer. It was cut for time, and because Vasquez wanted less action in this episode. However, the scene was fully animated and was uploaded to Youtube, but the video was claimed.
One cut moment involved fire sweeping cars away from a street.
Ms. Bitters' Valentine
When Miss Bitters says: I had a valentine once..., there was a plan for a thought bubble to appear over her head where a bunch of tentacles dissolve in next to Bitters, then is cut off as the phone rings. It is unknown why it was cut.
The lost 30 minutes
These lost moments entailed ZIM's 48-hour chase with the ham demon. Nickelodeon however didn't want an hour-long special, so this was cut.
Skool Bus sucked in!
One deleted scene involved a skool bus falling into the wrinkled Earth, this was cut for time but can still be seen in the DVD animatics.
Zim originally was to kiss Tak's hand and hug her, but Vasquez disapproved of any romance between the characters in the series, so it was not animated. However, these scenes can still be seen in the Animatics on the 2004 DVDs.
The explosion was originally red and fireball-like, but was changed to green due to the 9/11 attacks.
Iggins was supposed to die (again). Of course, Nickelodeon did not allow this.
When Red says, You! Save the donuts! Purple looks into the camera in an odd way. Originally, a doughnut was going to hit the camera, leaving crumbs on the lens. Purple was going to lick the doughnut crumbs off the lens, but it was cut. You can still see this on the animatics on the 2004 DVDs.
Bloody GIR was Born!
GIR was supposed to be covered in blood in the scene where Zim enters the library and sees his rampant robot surrounded by chaos. Nickelodeon thought it was too explicit and thus, Bloody GIR was born.