Shortly after the cancellation of The Angry Beavers, Horvitz was brought in as a potential voice of Zim, and was asked to record over certain lines for the pilot.

The Irkens want all the races of the universe to serve under their already vast empire, so they plan to send their elite soldiers to make the planets vulnerable so their forces can easily conquer them.

Former Irken Invader Zim, who had singlehandedly ruined the original Operation Impending Doom by stealing a battle mech and unwittingly annihilating a portion of his home planet, Irk, arrives uninvited.

On Earth, a boy named Dib intercepts a signal and hears about the empire's plans, though no one, these being his sister and father, takes any interest.

[2] Vasquez indicated that in the final version of the series, very little of his writing style was changed, other than restricting language and certain visuals that may not be suitable for children, including that of visuals deemed by the network as similar to the September 11 attacks[2][3] The biggest difference that he cites is the change from working alone to working with thousands of people at Nickelodeon, calling it an "absolute misery".

[3] A pilot was originally pitched to the network in 1999,[2][4] which featured many similar elements from the series, including a mysterious portrait of a monkey hanging in Zim's house.

[8] "The Nightmare Begins" was well-received overall by television critics, and was included alongside various other Nicktoons in a Wal-Mart exclusive Nickelodeon release, Nickstravangaza!

[9] Mac McEntrie of DVD Verdict commented positively on the episode, praising the "Great Assigning", and "Doom song" scenes, as well as the creation of Zim's house.

[13] That same year, Steve Ressel, Jhonen Vasquez, and Mary Harrington won the World Animation Celebration award for Best Title Sequence.