Invasion of the Thornberrys is the one-hour special and the season finale of The New Adventures of The Wild Thornberrys.
A brutal battle between the Australian animals and their alien clones erupts, although Darwin and Irwin refuses to fight with their alien clones resorting to slapping them (Marvin's alien clone also seems to refuse to fight, causing the original Marvin to ponder on what the two sides have in common).
The Thornberrys are unable to bear this senseless violence, even while Jack and Z grow tired but continue fighting. In an attempt to put an end to the ordeal, Z sums up all his remaining power for one final duel. However, just as he opens fire, Eliza runs between Jack and Z in a brave attempt to stop the fight. Z's attack hits Eliza, killing her.
Darwin, Irwin, and Marvin runs to Eliza's side and tries to wake her up. Darwin tries to revive Eliza, while the other animals, Debbie, Donnie, Nigel, and Marianne look on. After several attempts to revive Eliza, Darwin grows tired and stops. Realizing that Eliza is dead, Darwin, Irwin, and Marvin starts crying for their fallen friend, the other animals and their alien clones doing the same. Jack however, uses her DNA to revive her. Overjoyed, Darwin, Irwin, and Marvin leaps into Eliza's arms as the four embrace, happy to be reunited once again.
As everyone rejoices, Z, taken aback by Eliza's act of selflessness to save all the animals, has an epiphany over the relationship between man and beast, and realizes that the circumstances of how one is born should not be allowed to divide anyone. He leaves with his henchmen and the cloned animals, erasing everyone else's memory of the horrifying incident, knowing it is for the best.
Eliza and her family find themselves back at the gas station with no idea how they got there. Eliza looks up to the sky and spots Z flying past.
- Lacey Chabert as Eliza Thornberry
- Tom Kane as Darwin
- Jason David Frank as Irwin
- Bill Farmer as Marvin
- Flea as Donnie
- Danielle Harris as Debbie Thornberry
- Tim Curry as Nigel Thornberry
- Jodi Carlisle as Marianne Thornberry
- James Earl Jones as Z: The main antagonist of the special. He is an genetically engineered gray alien that escaped from a Government Facility near Sydney, Australia along with other genetically engineered aliens. He questions the meaning of his life due to the circumstances of his birth and strikes back against humanity to prove his own worth. Possessing great psychic power, he is able to manipulate the weather, control the minds of others and verbally communicate telepathically.
- Nolan North as Koba: A powerful yet very overconfident genetically engineered reptilian humanoid-like alien (resembling a bodybuilder) known as a Squamatian. He was rescued by Z along with the other genetically engineered aliens and in return he greatfully serves as Z's warrior. He is also shown to be a very skilled sword fighter.
- John DiMaggio as Killer: An idiotic genetically engineered cat-like alien known as a Lyran. He was rescued by Z along with other genetically engineered aliens and in return he greatfully serves as Z's warrior. He is also partner to Koba when fighting.
- Kari Wahlgren as Vitani: A ruthless and dangerous genetically engineered bipedal bee-like alien known as a Hexanthon. She was rescued by Z along with other genetically engineered aliens and in return she greatfully serves as Z's warrior. She frequently fights alongside Koba.
- Dee Bradley Baker as Stein: A shy genetically engineered tapir-like alien known as a Trunkinaspian. He was rescued by Alien Z along with other genetically engineered aliens and in return he greatfully serves as Z's scientist.
- Kevin Michael Richardson as Babun: A dim-witted genetically engineered baboon like alien called a Samian. He was rescued by Alien Z along with other genetically engineered aliens and in return he greatfully serves as Z's sidekick. He is also Zindros's sidekick.
- Tom Kenny as Zindros: An intelligent genetically engineered fox like alien called a Vulpian. He was rescued by Alien Z along with other genetically engineered aliens and in return he greatfully serves as Z's sidekick. He is more intelligent of a dim-witted duo consisting him and Babu.
- Jeff Bennett as Jack Smith: A debonair and charismatic tourist guide and an old friend of Marianne Thornberry who is secretly an Australian CIA Agent who is working undercover. He secretly knows about Eliza's power to talk to animals, and leads an army of animals to battle Z and his army.
- Jim Cummings as Ted: A koala who helps Eliza deal with the aliens by battling his alien clone K04L4.
- Jim Cummings as Fang: A saltwater crocodile who helps Eliza deal with the aliens by battling his alien clone CR0C.
- Adam Garcia as Roger: A red kangaroo that is going through a mid-life crisis after his only son Giam got eaten by Zander's pack, and has a great hatred for him. He helps Eliza deal with the aliens by battling his alien clone R00.
- Isla Fisher as Nya: A wedge tailed eagle who is feircly protective of her young. She helps Eliza deal with the aliens by battling her alien clone F1Y
- Denis Leary as Zander: A dingo who's pack ate Roger's son Giam. He is unaware of Roger's hatred for him and thinks he is delurious. He helps Eliza deal with the aliensby powering his alien clone D1NG0
- John DiMaggio, Kevin Michael Richardson, and Keith Ferguson as Harold, Frank, and Pete: A trio of razorbacks who help Eliza deal with the aliens by battling their alien clones B0ARs
- Hugh Jackman as Horner: A water buffalo who helps Eliza deal with the aliens by battling his alien clone BUFALL0. Horner has seen the effects of other invasive species like him and thus battles the aliens with as much power as he can force.
- Steve Carell as Slasher: An emu who helps Eliza deal with the aliens by battling his alien clone F0WL. He is also Horner's best friend.
- Andy Dick as Iggy: A perentie who helps Eliza deal with the aliens by battling his alien clone L1Z4RD.
- Charlie Adler as Hiss: A inland taipan who helps Eliza deal with aliens by battling alien clone B04.
Animals Featured in this Episode
- Australian Water Buffalo
- Inland Taipan
- Red Kangaroo
- Saltwater Crocodile
- Wedge Tailed Eagle
- Z has similarities to Mewtwo from Pokemon: The First Movie. Both are genetically engineered, they question the meaning of their lives due to the circumstances of their birth, both attempted to strike back against humanity to prove their own worth, both created an army of clones, and both change their ways at the end and erase everyone's memory.
- The plot of the special is inspired by Pokemon: The First Movie.