Since Doctor Who materialized back onto screens in 2005, there have been three different showrunners and as a result, three distinct eras of the show. When Steven Moffat took over in 2010, he decided to heavily lean into the "timey-wimey" aspects of Doctor Who and abandoned Russell T. Davies' more grounded approach.
Moffat created some memorable story arcs while he was at the helm such as the crack in time, the Doctor's apparent death, and Missy's identity. The showrunner brought back his previous creations The Weeping Angels and River Song but also made some memorable new additions to the Whoniverse such as the Silence and Amy Pond.
"The Eleventh Hour"
Moffat's era opens with this beautifully shot, fairytale-inspired episode which sees the newly regenerated Doctor crash land in Amelia Pond's back garden. Having the Doctor meet his next companion as a child first is a unique and refreshing way to introduce them.
While the villain of the episode isn't particularly memorable, Matt Smith hits the ground running with his incarnation of the Doctor. Some Doctors take a while to truly win the audience over but Smith had most fans convinced from the off. The fairytale vibe of the episode and the season as a whole ensure it stands out and excellently introduces Moffat's vision for the show.
"The Impossible Astronaut"/"Day Of The Moon"
By season 6, fans had become used to epic two-part finales but this season changed things up and began with a two-part premiere instead. Early on in the story, the Doctor's companions witness his apparent death at the hands of a mysterious astronaut.
The stakes are higher than ever in these episodes and it's a great way to get fans hooked right from the beginning of a season. The story also introduces the terrifying Silence who had been teased at the beginning of the previous season. Some of the scenes with the Silence are genuinely creepy and even if the later payoff is quite disappointing, the mystery setup surrounding the Doctor's death makes for a compelling start to this arc.
"The Time Of Angels"/"Flesh And Stone"
After season 3's "Blink," which is considered one of the scariest episodes of Doctor Who, many fans hoped that Moffat's original creations, the Weeping Angels, would return in his era. The now-iconic monsters make their long-anticipated return in this exciting two-parter from season 5.
The story also sees the Doctor come face to face with River Song again, continuing the mystery set up in the previous season. While this is certainly not as strong as the Angels' original outing, the monsters are well utilized and Amy's ordeal is particularly harrowing to watch. Seeing the Angels in a completely different setting is refreshing and the clever inclusion of the "crack in time" story arc also makes this one of the most memorable stories in this era.
"Heaven Sent"
This episode is often considered the Twelfth Doctor's best due to Peter Capaldi's stellar performance. For the most part, the Doctor is alone in this episode, which means Capaldi has to carry it all by himself and he does a perfect job.
Even without the presence of companions at the Doctor's side, it is still one of the most engaging episodes of this particular season. Capaldi's monologues and the stalking Veil behind him create a perfect exploration of grief. While this episode is certainly better watched in isolation due to the underwhelming "Hell Bent" that follows, it does perfectly explore the Doctor as a character like never before.
"Vincent And The Doctor"
This season 5 episode sees the Doctor and Amy meet Vincent Van Gogh, who is being pursued by an alien creature that no one else can see. Those around Vincent dismiss him as "mad," but the Doctor and Amy are able to see the real him as the story progresses.
In a particularly emotional scene from the episode, Vincent goes to the future to an art gallery where he's able to see the impact his work has had. The story stands out in particular as it puts a spotlight on mental health with the invisible creature acting as a metaphor for depression. The ending when Amy realizes they were still unable to save him is truly heartbreaking, but the Doctor's speech about good things and bad things makes this a fitting close for the episode.
"Under The Lake"/"Before The Flood"
Season 9 experiments with the formula and structure of the show, and "Under the Lake" and "Before the Flood" make up one of the best two-part stories from Doctor Who. What starts off as a typical base under siege plot soon turns into something much more.
The story sees the Doctor and Clara pursued by "ghosts" and explores the fascinating concept of the bootstrap paradox as well as the intricacies of time travel. The image of the Doctor as one of the ghosts is haunting and the Fisher King makes for a superbly intimidating villain. In a particularly divisive season of the show, this story is certainly a standout.
"The Doctor's Wife"
Season 6 sees critically acclaimed fantasy writer Neil Gaiman writing this episode. While it has been long established that The TARDIS is sentient, the Doctor has never had the chance to properly interact with his beloved time machine before this.
In "The Doctor's Wife," the TARDIS is targeted by a malevolent entity named House, who is one of the best low-key villains from Doctor Who. Following this, the time machine's consciousness enters the body of Idris. The episode features some beautiful interactions between the Doctor and Idris and her characterization is perfect. These emotional scenes are also perfectly counterbalanced by the terrifying ones where Amy and Rory are trapped inside the shell of the TARDIS and manipulated by House.
"The Day Of The Doctor"
This special episode celebrates the huge milestone that is Doctor Who's 50th anniversary. The story sees the incumbent Doctor, Smith, coming together with two of his previous incarnations as played by David Tennant and the late John Hurt.
Since the show's revival in 2005, the Time War has been a significant and recurring plot point, but it was during this episode that fans were finally able to see these events onscreen. The interactions between the three Doctors in the story are hilarious as their differing personalities both clash and complement each other. "The Day of the Doctor" has become iconic as it features returning cast members, the explosive Time War, The Zygons and the Daleks and, in some capacity, all 13 of the Doctors up to that point.
"The Girl Who Waited"
At times, the Moffat era becomes heavily focused on complex plot lines and complicated story arcs, but this season 6 episode is a refreshing character study of companions Amy and Rory. When Amy first joins the TARDIS, her treatment of Rory is questionable, to say the least, and their relationship seems fragile. However, as things progress, their relationship goes from strength to strength until the two would do anything for each other.
In fact, the older Amy in this episode feels so hurt by Rory's "abandonment" of her that she has grown bitter and cold. Seeing the Doctor forcing Rory forced to choose between the two versions of his wife is gut-wrenching and ensures the audience is fully invested in the couple's relationship going forward.
"World Enough And Time"/"The Doctor Falls"
The final story of season 10 is arguably the 12th Doctor's best and is one of the strongest Cyberman stories in Doctor Who. The Doctor and his companions find themselves on a ship where time runs differently from one end to the other.
Early into the first part, Bill is shot through the stomach in a shocking moment and her body is taken to the other end of the ship where she is "upgraded" into a Cyberman. For the first time onscreen, this story also features two different incarnations of the Master and highlights Missy's internal struggle as she questions whether she can truly become a better person. The episodes are suitably epic and could have provided a fitting and appropriate ending for the 12th Doctor's tenure on the show.