With Jodie Whittaker set to make her departure from Doctor Who in a couple of months, many fans have begun debating as to how she will be written out. Since it has been revealed that she will not be regenerating inside the TARDIS (via Radio Times), breaking the long tradition set up in the New Who series, there is a whole new level of excitement (and suspense) as viewers will have to wait to see which villain may cause the final blow.
Although the Doctor has always been an intelligent hero with a tenacity for thinking outside the box, the Timelord is not always the immediate victor. Part of what makes the Doctor such an endearing character is that they will not always win. They may win later again down the line, but they are often given the greatest teacher of all: failure. These failures and temporary losses have come from some of the most iconic villains in the Doctor Who franchise.
The Zygons
These tentacled monsters have the ability to shapeshift, which makes them hard to find. Though the Doctor is clever and manage to win most of the time, the Zygons have been a thorn at his or her side for hundreds of years. One of their more impressive feats came in the Doctor Who 50th Anniversary special, The Day Of The Doctor.
They not only took the form of the Queen centuries in the past, but they also took over the organization UNIT, threatening the lives of millions in the process. Even though the Doctor was able to reason with them, it took the Doctor three different times to get the job done.
The Midnight Entity
This is one of those rare times when even the Doctor himself did not win against a threat. In the Series 4 episode "Midnight," the Doctor and several strangers are trapped on a bus with a strange entity that begins to torment them.
Nobody is safe, and it leads to paranoia getting the better of characters, not too dissimilar to what the many characters go through in John Carpenter's The Thing. Even the Doctor becomes possessed by this entity at one point, despite all efforts from the Time Lord to stop him. Instead of the Doctor, it's actually one of the strangers who end up saving the day on their own.
The Silence
It's both surprising and not surprising that this race of aliens took over the planet Earth without the Doctor noticing. These beings are unique due to their aural ability: anyone who sees them immediately forgets them once the Silence are out of their sight.
This ability allowed these terrifying Doctor Who monsters to infiltrate Earth and conquer it from the inside. However, the Doctor did find a way to stop the alien beings, but that doesn't stop their control of Earth for decades from being a commendable task for a villain.
The Great Intelligence
The Doctor defeated The Great Intelligence in their first encounter, but the telepathic entity does not give up easily. In fact, it waited centuries and plotted out its revenge; waiting until the right moment to find the grave of The Doctor in order to access his timeline.
The Great Intelligence nearly won, going back in time to ensure that every victory the Doctor had was turned into a defeat. It would have killed the Doctor if Clara hadn't gone into the Doctor's timeline and fixed everything, thus defeating The Great Intelligence.
The Cybermen
Since the earliest days of Doctor Who, the Cybermen have been some of the Doctor's greatest rivals. They've nearly won against the Time Lord multiple times over the years in his various regenerations.
One time the Doctor was tricked and nearly turned into a Cyber Planner, and in another sad time with Peter Capaldi's 12th Doctor, they allied with Missy to create a new army of Cybermen right below London. Even in the Classic Doctor Who episodes, the Cybermen were troublesome opponents, such as when they murdered one of his companions: Aldric.
The Daleks
The Daleks are arguably the Doctor's most iconic foe. They have been a threat since the 1st Doctor era of Doctor Who, and they continue to be with the 13th Doctor. The Doctor has a personal hatred for them, for it was the Daleks who waged war with Gallifrey that forced the Doctor to destroy them and his own kind to stop them.
Multiple times, the Daleks have invaded Earth, only for the Doctor to save the day. They even nearly killed the Doctor in the past, such as with the Ninth Doctor only for companions to save the day.
The Vashta Nerada
In most cases, the Doctor can be outsmarted or beaten by villains; usually, the Time Lord's or the companions always finds a way to win in the end. However, this is usually not the case with the Vashta Nerada (which has only appeared in one episode and fans will dread the episode it ever returns in).
It's a living shadow that devours its victim and then possesses them as a walking skeleton. The only thing that the Doctor could do was delay the creature until he and any survivors could escape; this unfortunately cost him the life of the ever-quotable River Song, his wife.
The Weeping Angels
These intergalactic beings are some of the scariest monsters to meet the Doctor; they only move when no one is looking. When they touch someone, they send them back in time to a point where they would live out the rest of their lives and die without seeing their loved ones again whilst feeding on that lost time.
This twisted method is what they use on the Doctor, sending both Amy Pond and her husband Rory back in time. A revenge against the Doctor for defeating them, which became one of the saddest farewells to a companion in the whole series.
The Master
The Moriarty to the Doctor's Sherlock Holmes; the Master is a fellow Time Lord, but one that is pure evil. They love to torment others, specifically the Doctor by either taking over the world several times or committing mass genocide. Due to being a Time Lord with the same regenerative properties, the Master has deceived the Doctor more than a few times thanks to their new faces.
Other times, they have survived death much to the Doctor's shock and committed atrocities as a puppet master for other villains. Even with the most recent incarnation of The Master played by Sacha Dhawan, The Master manages to pull the rug from under the Doctor.