Across 60 years of television, the Doctor has used his wits to defeat a variety of foes. Whether they be Daleks, ordinary humans, or godlike beings, the Doctor has triumphed over nearly all of them.
Despite the Doctor's victories against his foes, many of them still give the Time Lord a run for his money. The Master in particular has proven himself an intellectual equal to the Doctor a number of times, and with him set to return for the Thirteenth Doctor's final adventure, it'll be interesting to see how he or any other villain might outwit the Doctor. In honor of the scheming intellectuals that will pepper the specials, now is the perfect time to comb through Doctor Who's smartest villains.
The Cybermen
Driven by cold, hard logic, The Cybermen were Doctor Who's answer to the advancement of spare-part surgery in the 1960s and the fears that came with losing identity. In most of their adventures, the Cybermen seek to convert other humanoid creatures into Cybermen to keep their race alive.
While the Cybermen's near robotic presence and personality have resulted in a species that can outthink many others, their lack of emotion makes them unprepared for the irrationalities of human behavior. Clever as they are in luring people into their tombs and manipulating the Doctor into giving up valuable technology that would help the Cybermen, they've never been able to overcome the emotion driven minds of the TARDIS team.
The Monks
Introduced in Doctor Who series 10, the Monks are an alien race bent on controlling Earth via manipulation. To this effect, they planned out their invasion using a virtual simulation to parse out any threats.
While the Twelfth Doctor was able to prevent their initial plan of taking over via the use of a fatal man-made bacterium, they still managed to assume control due to Bill accepting their offer to save the Doctor. Even when they were driven from Earth, they got away without damage by wiping the planet's memory of them.
The Rani
A peer of both the Doctor and the Master, the Rani was a renegade Time Lord who enslaved peoples and planets to conduct her amoral experiments. The most notable of these involved the creation of a superbrain using some of Earth's smartest minds.
Beyond her abilities as a brilliant neurochemist and biologist, the Rani also used her intellect to manipulate the Doctor into helping her. In "Time and the Rani," she was able to trick the recently regenerated Seventh Doctor into thinking she was his companion, Mel, and almost got him to help complete her experiment had the real Mel not intervened.
The Great Intelligence
Introduced in the 1966 story, "The Abominable Snowmen," the Great Intelligence was a mysterious collective that lacked a corporeal form but could control deceased bodies and mechanical beings. It famously sought to make the Doctor's intelligence a part of its own before deciding the Doctor was too great a threat to its machinations and attempted to erase the Doctor from history.
What makes the Great Intelligence such a formidable foe is the fact that it, unlike so few Doctor Who villains, learns from its mistakes. From operating out in the open to lurking in the shadows, the Great Intelligence adapted to match the Doctor's wits. Eventually, it came to the conclusion that the Doctor's victories must be undone and managed to contaminate the Time Lord's timeline by kidnapping the Eleventh Doctor's friends.
The Krillitanes
Headed by the charismatic Lassar, The Krillitanes were a race of aliens that took on the attributes of species they had conquered. In their sole television appearance, they infiltrated a high school and used the children to crack the Skasis Paradigm, a mathematical equation that explains how the universe works
Though their plan was very low-key in comparison to other alien threats who wished to conquer the universe, the Krillitanes nearly succeeded because they chose to not draw attention to themselves. Were it not for Mickey ing the Doctor, they might have succeeded in obtaining the secrets of the universe.
The Daleks
The Doctor's oldest foes are not only his most vicious, but also among his smartest. One need look no further than the stellar episode "Dalek" where a single Dalek is able to manipulate Rose Tyler into freeing it and wreaking havoc on the underground base it was chained up in.
When acting as part of a larger unit, the Daleks have shown their ability to take over space colonies, outmaneuver the Time Lords in the Time War, and imprison the Doctor in the Pandorica. Were it not for their extreme ideology and arrogance, they would have exterminated the Doctor a long time ago.
Rassilon
One of the founders of Time Lord society, Rassilon helped develop time travel along with Omega (who he supposedly betrayed). Long after his death, he was resurrected by the Time Lords to lead them in the Time War, where he attempted to bring Gallifrey out of the war using the Master.
Perhaps the greatest indicator of Rassilon's genius can be found in his creations and artifacts. He was famously involved in the creation of the Hand of Omega and the living metal known as Validium, items that Doctor Who's most notorious foes have attempted to harness without success due to the complex nature of the constructs.
Omega
The Time Lord most instrumental in developing time travel, Omega was cast off into an anti-matter dimension when his experiment to harness the power of a black hole backfired. Trapped in this reality with himself in control of its fabric, he slowly set about to return to his home dimension.
While Omega's intelligence comes into question considering how he failed to harness the power of time travel, the Time Lord still boasted an intellect far greater than most of his peers. In "The Arc of Infinity," he was able to create a corporeal form for himself and inhabit the Doctor's universe for a brief period of time (before he was erased by the Doctor) and in the audio drama Omega, he was able to take control of the Doctor's body without him knowing.
The Master
The Doctor's arch nemesis is one of Doctor Who's most conniving characters. For 50 years, the Master has been scheming to take over planets and kill the Doctor, and every time, they've come back despite the odds being stacked against them.
Perhaps the Master's greatest show of intelligence can be found in the Russel T. Davies' era of Doctor Who, when he manages to steal the Doctor's TARDIS and become Prime Minister of Great Britain. His ability to create a new identity for himself led to the Master taking over the world, something few Doctor Who villains outside the Daleks have been able to accomplish.
Davros
The creator of the Daleks, Davros is among the most intelligent beings in the Doctor Who universe. Through his actions, he managed to win the war on Skaro, and has survived for thousands of years thanks to his life- technology (which he created).
The ultimate proof of Davros' formidable intellect can be found in the Daleks' efforts to revive the mad scientist on at least three separate occasions. Despite their disgust for their creator, the Daleks realized that their "genetic superiority" was no match for Davros' brainpower, and he was able to use it to keep himself alive long after the Daleks' lost use for him.