Intellectually Supported Tyranny aka: Trahison Des Clercs
This references a general idea that intellectuals are supposed to be responsible in their social and political opinions, but has a more general application to the phenomenon of such people becoming (at best misguided) sympathizers of the Evil Overlord du jour. In fiction, this is a good variation on Not Brainwashed. Given that they tend to reference actual totalitarian governments, dystopian works often have the heroes interacting with this type, who tends to have power in a paradoxically anti-intellectual state.
Kiyomi Takada has this kind of vibe in Death Note, being an important example of a sane Kira supporter who is established to be on the same intellectual level as Light (albeit only academically). In her profession as newscaster, rather than helping to secure society against the Kira-cult, she becomes one of its major propagandists.
Aldous Huxley's Brave New World has a rare example of this character as the Evil Overlord himself, in Mustapha Mond. Also unique though is that he comes across as more complex/likely to be right than other examples.
Fahrenheit 451 has Beatty, who is Da Chief for the Firemen and typically of a dystopian novel, is a well-read intellectual devoted to his job of burning books. It's implied in the novel and more explicit in some adaptations that at heart, Beatty hates himself for what he has become.
This type is very common in literary works with 19th-century anarchist characters, the originators of the Terrorists Without a Cause idea. This character is generally someone with a good knowledge of chemistry who applies it to arm the anarchists with explosives.
In his novel Under Western Eyes as well as at least one short story, Joseph Conrad has a character called the Professor. It's been noted that this was a somewhat unfair presentation of one of Conrad's friends from the Rossetti family (the same as Dante Gabriel and Christina), who, while politically radical and a chemistry expert, was not involved in terrorism.
The play The Firebugs (also translated as The Arsonists) has the title pyromaniacs aided by a character identified only as Professor.
In Ragtime, one of the sons from the main family of wealthy WASPs starts out by making fireworks and ends up in this role in the actual anarchist movement (e.g. with Emma Goldman), but is presented sympathetically, more along the lines of He Who Fights Monsters. This contrasts with other "Professor" characters who lean in the direction of simply enjoying things going boom despite a basis in radical politics.
In The Wheel of Time, the leader of the Forsaken was once a philosopher - and since the Dark One will destroy time forever if he succeeds and gets to keep trying until he manages, decided to throw his lot in with the winner.
In fact, almost all of the Forsaken were intellectuals before the Bore was opened. Sammael (an athlete), Moghedien (investment broker) and Be'lal (lawyer) were not (and Rahvin is a cypher), but the Forsaken include a doctor, a geneticist, a composer, a university lecturer, a psychiatrist, an academic mage studying the nature of magic, an historian/anthropologist, and the aforementioned philosopher. The others are mostly well-versed in history, literature, and especially magic, amongst other things.
Keep in mind that these are the surviving Forsaken, during the original War of Power the term Forsaken was used to describe any Channeller who sided with the Dark One. These thirteen Forsaken survived out of sheer luck, being in Shayol Ghul when it was sealed.
Atlas Shrugged has a handful of 'intellectuals' supporting the People's States, although the overwhelming majority are unwilling to put forward works stating anything more than uncertainty. Dr. Ferris, author of Why Do You Think You Think and political force behind creating Project Xylophone with a range focused within the continental United States, is the most overt of that branch. Dr. Stadler is the more conventional intellectual, and his brilliance lends to a couple Pet the Dog moments, before we discover exactly what he was willing to sell his word and his soul for.
Pretty much every totalitarian movement from the French Revolution to the present day has had prominent intellectual supporters.
Doctor Wallace Breen in Half-Life 2 acts as the voice and face of the alien Combine occupation, but it's not entirely clear if his support is out of self-serving misanthropy or actual misguided idealism. Regardless, he constantly tries to provide "rational" and "scientific" reasons for why aliens committing genocide and suppressing human reproduction is a good thing for our future.