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- Team Quest
- Jade Kenyan-Bannon (single appearance)
- Dr. Zin (dies)
- Replicants (only appearance; dies)(no lines)
- Snipe (only appearance; dies)(no lines)
- Dr. Vincent Devlon (only appearance; dies)
- Commander Burns (single appearance)
- 3-DAC (single appearance)
- President of the United States (single appearance)
- Leonardo da Vinci Template:Green
- Dr. Zin clone (first appearance)(no lines)
- Intelligence 1 Record Facility
- Quest Headquarters
- Police department
- United States
- Intelligence 1 Headquarters
- Rain forest
- Dr. Zin's headquarters
- Europe Template:Flashback
- Iraq Template:Flashback
- Cambridge University (mentioned)
- Tokyo, Japan
- Tokyo Airport
- Paris, France
- Eiffel Tower
- China Template:Flashback
- Rome, Italy
- Questor 1
- Several changes to the continuity have been made that don't fit and make little sense (most of which were later dropped in The Real Adventures of Jonny Quest):
- Jonny's mom is now on the team, as if it's a prequel, only Race and Hadji are also on the team. Race was only with the team because of Mrs. Quest's death, which was talked about in the first episode of the original series, The Mystery of the Lizard Men.
- Jade is now Caucasian with long red hair. She has also been married to Race and bore their child which he had no knowledge of.
- Jessie Bannon is based on the scrapped idea of having the almost identical Jessie Bradshaw from the 80's series episode, Deadly Junket, as a recurring character (that episode's plot is recycled, albeit with a twist, for this movie). Having Jade and Race as a team is also another idea scrapped from the aforementioned series.
- Jonny and Hadji didn't know who Jade was.
- Zin has been turned into a withered and diseased old man, with liver spots.
- The fact that the original Zin dies in this, only for his clone to survive at the end, would suggest that the Zin in Jonny Quest Versus the Cyber Insects is his clone, but this isn't elaborated on. The Quest team don't even question his survival, perhaps because they're used to it.
- Although this film has been ignored in regards to Jade being Jessie's mother, Rachel's name resurfaced in the Real Adventures episode, The Edge of Yesterday, as the name for a time travel computer program for Quest World.
- None known.
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