A character whose passion is fiddling about with chemistry sets... has taken a dark turn. In Real Life, the term "clandestine chemistry" refers to any chemical science that's being done in secret for illegal means — usually (in fiction, almost exclusively) manufacturing drugs. Expect the Clandestine Chemist to work out of a dingy little lab — trailers and garages seem favorites — and to broker his wares to the local crime kingpin, with all the drama that typically accompanies a career in organized crime. However, it's not impossible for heroic types to have a need for their services.
These characters are likely to overlap with Mad Scientist, especially if they've been dipping into their own supply. On a sliding scale of criminal unpleasantness, this character is usually placed slightly higher than the Playful Hacker, probably because Drugs Are Bad. (And messing around with chemicals unsupervised is usually a bad idea, for both legal and safety reasons.)
- One Piece: Caesar Clown used to be a legitimate scientist for the World Government until he faked his own death. For the last four years, he's hidden inside his mostly abandoned island lab, working on chemical weapons to be sold to the "underworld" and other shady projects.
- Post New-52, Batman learned chemistry skills from an exiled Russian professor named Sergei.
- In a comic book story based on the 1990s Back to the Future cartoon series, one of Marty McFly's relatives was a chemist working for one of Biff Tannen's relatives back in the Roaring Twenties making illicit alcoholic products during the Prohibition period. His talents were used to help create a medicine for Doc Brown's dog Einstein who came down with an eye disease that made him see cats everywhere (Doc called them "cat-aracts"). Marty's relative decides to make a clean break from his past after he succeeds (and after Marty deals with Tannen's gang) and move to Hill Valley.
- Boogie Nights has protagonist Eddie Adams living with lowlifes and parolees in Los Angeles. Todd Parker inveigles Eddie into coming with him to sell a bag of baking soda to Rahad, who has "more money than God." While Rahad is haywire stoked on cocaine, he has a bodyguard and chemist on hand. This fellow begins taking a sample of Todd's wares for analysis, which compels Todd to begin an armed robbery. The chemist is shot in an exchange of gunfire.
- Michael Newman of Jacob's Ladder was a clandestine chemist making LSD before becoming a Reluctant Mad Scientist for the US Army in Saigon.
- Zig-zags on Buffalo Soldiers with Military Moonshiner, as Ray Elwood makes heroin in a military base.
- The Serpent and the Rainbow: Mozart makes poisons and paralyzing devices that he sells to kill people, although the "clandestine" part is downplayed, since whole bars full of people in the poorest part of town observe him making deals.
- The Anarchist Cookbook is a book containing recipes on how to make explosives. The methods described in the book are so poorly thought-out and dangerous, it's been suggested it was written as disinformation and possibly intended to make potential bombers blow themselves up!
- Rogue has a couple who make meth in their house and force their sons to buy Sudafed for them, act as lookouts, and help with dangerous reactions. In the end, Kiara's dad calls CPS on them. They try to destroy the evidence by pouring it down the drain, blowing up their house, and severely maiming both of them.
- Breaking Bad is about a humble chemistry professor who turns to meth production as a way of supporting his family after he learns he has cancer. This gets more explanation when it's revealed that he used to be quite a talent in his field but sold out his share of his (now massively successful) chemical company when his girlfriend got pregnant.
- On Almost Human, Rudy goes undercover as this type of character.
- Sherlock's new protege, Bill Wiggins, is a skilled chemist who used to waste his gifts on getting high. Now he wastes his gifts as Sherlock's replacement flatmate but has proven useful by making a sedative that works rapidly without causing long-term harm to those it's used on.
- The Leech playbook in Blades in the Dark naturally gravitates towards this archetype, between their default starting ability Alchemist (which allows them to research and to mix alchemical concoctions) and their signature item being a pair of bandoliers for carrying vials with alchemical substances for every purpose. The "clandestine" part comes from the fact that player characters in Blades are members of a criminal gang working under the authorities' noses.
- Chronicles of Darkness
- One conspiracy in Hunter: The Vigil is the Ascending Ones, an ancient order of alchemists who fund themselves in modern times through the drug trade. They've probably got one or two of this trope on the payroll.
- One of the Vampire: The Requiem books details an NPC called Leland Bancroft, a chemistry prodigy who used to make drugs for his gangster-vampire-dad until joining the Lancea Sanctum. One recommended storyline is having his old employer come looking to get him back.
- Far Cry 3 introduces us to Dr. Alec Earnhardt, who's been hiding out on the Rook Islands for a while, studying the local plants to develop new hallucinogens. He's also been testing them on himself to drown out the grief of a dead loved one, so he's pretty detached from reality.
- Hitman 2: Jorge Franco, the Delgados' chemist, wants to develop a "super-cocaine" for the cartel.
- In Mafia III, one of the crime rings you can break up or take over is the PCP lab based out of the city science center.
- Implied to be the case with your missing/deceased friend Casey in Night in the Woods, as one of his murderers refers to him cooking up meth with a cousin.
- PAYDAY 2: The gang end up having to improvise this role during the first day of the Rats heist. Their original plan was to protect a group of actual meth cooks but said cooks get offed by the Mendoza cartel, forcing the gang to make the meth themselves. Not properly listening to Bains instructions can cause the meth lab to be blown to kingdom come, which will either ruin the planned trade the gang were preparing for on lower difficulties or causing a Non Standard Game Over on higher difficulties.
- Moonshiners are those who unlawfully make distilled spirits, whether to escape alcohol excises or a prohibition.
- Due to the ease of the process, several persons, both gangsters and addicts, make meth in makeshift laboratories, causing several deadly accidents.
- Subverted by those Russian drug addicts who cook Krokodil without having the faintest idea of what happens in that process. The result is an impure and tainted concoction, which causes lesions, gangrene and deaths. The sad thing is that the good stuff in it - desomorphine - could be purified with two simple operations, of which the cooks have usually no idea.