An organization of scientists who protect mankind against the hidden and terrifying things of the world. There are:
Dr. Arthur Beeman
Dr. Arthur Beeman is a Secret Scientist who studies aliens and UFOs. However, far from being a conspiracy nut, his obsession is apparently justified as he saved the world from invasion by figuring out the 'crop circle code'. Beeman is often blunt and mildly insulting in his speech. He gives people nicknames based on their appearance (Zak's hair, for example, results in names such as "Skunk-do" or "Salt and Pepper"). Doc and Drew called him in to watch Zak, Fiskerton, Komodo, and Zon while they were away on their anniversary dinner. Drew has stated that in "The Underworld Bride" he's her "least favorite". In "Kur" Pt. 1, he is one of the Scientists after Zak (and gave him a new nickname "Franken-hair" and later in the season "Panda- head").
Dr. Paul Cheechoo
Dr. Paul Cheechoo is a Secret Scientist that specializes in cold-climate research. He and a team of experts travel the world studying strange geological anomalies. He's currently stationed at Ellef Ringnes. In one episode he mentions he grew up in cold weather, and he indirectly reveals at the end of "Where Lies the Engulfer" that he is from Canada. The Saturdays tend to cause, or at least get involved in, ecological disasters when they do any work near him, which he eventually points out with slight annoyance. He also has more of a sense of humor than the other Secret Scientists and seem to be the most friendly with Zak. He attended Van Rook's funeral.
Dr. Miranda Grey
Dr. Miranda Grey is a Secret Scientist who held a piece of the Kur Stone, until Munya stole it. She's an expert at quantum physics and works on particle acceleration in Antarctica with her robot sidekick, Deadbolt. She has a gun which can create miniature wormholes, allowing her to physically attack opponents from a distance. She is Abbey Grey's sister and was disatisfied that she sided with Leonidas Van Rook. In "Kur" Pt. 1, she is one of the scientists after Zak. In the "Thousand Eyes of Ahuizoti," It's revealed that She has been watching Weird World for surveillance (though she saved Zak in the season finale). She also attended Van Rook's funeral.
Deadbolt is a robot that is Miranda Grey's sidekick. In "Kur" Pt. 1 and "The Thousand Eyes of Ahuizotl", it assists Miranda in hunting Zak. It's a recuring pun that in every episode he appears in he gets distroyed only to come back later new and improved. Miranda also mentions that Dead Bolt costs 37 million dollars to repair.
Professor Talu Mizuki
Professor Talu Mizuki is a scientist who invented a mind-swapping device for (unknown to him) crime lord and philanthropist Shoji Fuzen. When asked to use it to implant the mind of one of Fuzen's men into a Hibagon, he takes the Hibagon's body himself. In the ensuing confrontation, his body is lost in a fire and the mind-swapping device destroyed. He attempts to take revenge against Fuzen, but is convinced by Doc to let it go. He now lives in a cave lab alongside his white tiger (mind-swapped with a dog) working on a way to get his mind back into his body and continue his research. Apparently, he has become a member of the Secret Scientists as shown in "Eterno" where he helps the other scientists solve the Eterno crisis. In "Kur" Pt. 1, he is one of the scientists after Zak.
Talu's White Tiger
White tiger is seen in the Vengeance of Hibagon as a pet of Professor Talu Mizuki. He is a dog brain in a white tiger. Zak states that it would be cool to have one but then, when growled at, says he is fine with the pets they have.
Dr. Henry Cheveyo
Dr. Henry Cheveyo is another Secret Scientist who held a piece of the Kur Stone. Argost stole it, then used a cryptid parasite to extract the location of the third piece from him. He works at the Mesa Observatory in Arizona. He was seriously wounded when he took the brunt of an explosion meant to kill the Saturdays, but survived.
Agent Epsilon and his 11-year-old "son" Francis are members of a secret organization loosely allied with the Secret Scientists, though they have their own agenda. Epsilon is usually quite serious and by the book, personifying the "Men in Black" archetype (in behavior if not appearance). He also has access to "the files" which is a large database on everyone and everything. He also has a group called his "people" for protection. It is revealed in "The Unblinking Eye" that he and Francis are actually clones of the "perfect agent" their organization found 100 years ago.
The 11-year-old "son" of Agent Epsilon. Francis is clever and manipulative, just like his "father". Francis wears a shield generator that shocks anyone who tries to touch him without permission. He and Zak have a rivalry, as evident in "Paris Is Melting" and "The Swarm at the Edge of Space". It was revealed in "The Unblinking Eye" that Francis and Epsilon are clones of a "perfect agent" their organization found 100 years ago thus explaining why he has no mother. Francis also explained that in time he will be given a "Francis" of his own to raise as Epsilon is raising him. He also showed a great disdain and bitterness over this fact, due to the massive amount of pressure it placed upon him. Zak tells him he's in charge of his own destiny and is his own person, not just another clone. Francis understands and allows Zak to escape instead of capturing him as a way to thank him (though he wouldn't admit it).