42 Best Doctor Who Story Arcs (2005-2013 Series)

These are my favorite story arcs of Doctor Who since the reboot in 2005.
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1.
Doctor Who (2005 TV Series)
Episode: The Impossible Planet (2006)
    1 2 3 4 5 6 7 8 9 10 8.8/10 X  
The TARDIS lands on an alien planet shrouded in a darkness that even the Doctor can't figure out. And what is lurking at the bottom of The Satan Pit? (45 mins.)
 
2.
Doctor Who (2005 TV Series)
    1 2 3 4 5 6 7 8 9 10 8.3/10 X  
The Ood have given a warning to The Doctor. The Master is returning yet that is not the biggest threat. A darkness is coming which brings with it The End of Time. (45 mins.)
 
3.
Doctor Who (2005 TV Series)
Episode: The Stolen Earth (2008)
    1 2 3 4 5 6 7 8 9 10 9.1/10 X  
The return of an old enemy leaves Earth along with 26 other planets stolen from their places. As the Doctor and Donna look for the whereabouts of Earth, former companions of the Doctor assemble a resistance against the new Dalek Empire. (45 mins.)
 
4.
Doctor Who (2005 TV Series)
Episode: Human Nature (2007)
    1 2 3 4 5 6 7 8 9 10 9.0/10 X  
In 1913, Martha watches in jealousy from afar as The Doctor learns what it is to be human and to fall in love with the local school nurse, Joan Redfern. (45 mins.)
 
5.
Doctor Who (2005 TV Series)
Episode: The Name of the Doctor (2013)
    1 2 3 4 5 6 7 8 9 10 9.2/10 X  
The Doctor's friends are being kidnapped, which leads him to the fields of Trenzalore, where his greatest secret will be revealed and Clara's mystery will be solved. (45 mins.)
 
6.
Doctor Who (2005 TV Series)
Episode: The Doctor's Daughter (2008)
    1 2 3 4 5 6 7 8 9 10 7.8/10 X  
Caught in the middle of a war between the Humans and the Hath in the planet Messaline, the Doctor finds himself once again a father. (45 mins.)
 
7.
Doctor Who (2005 TV Series)
    1 2 3 4 5 6 7 8 9 10 9.3/10 X  
The Doctor, Mickey and Rose land on a spaceship in the 51st century only to find 18th century Versailles on board, the time of Madame De Pompadour! To find out what's going on the Doctor must enter Versailles and save Madame De Popmpadour but it turns into an emotional roller coaster for the Doctor. (45 mins.)
 
8.
Doctor Who (2005 TV Series)
Episode: Vincent and the Doctor (2010)
    1 2 3 4 5 6 7 8 9 10 9.3/10 X  
The Doctor and Amy travel back in time to meet Vincent Van Gough and face an invisible monster that only the painter can see (45 mins.)
 
9.
Doctor Who (2005 TV Series)
Episode: The Girl Who Waited (2011)
    1 2 3 4 5 6 7 8 9 10 8.6/10 X  
Amy is trapped in a quarantine facility for victims of an alien plague which could kill the doctor in minutes if he were to catch it... (45 mins.)
 
10.
Doctor Who (2005 TV Series)
Episode: Bad Wolf (2005)
    1 2 3 4 5 6 7 8 9 10 8.7/10 X  
Jack, The Doctor and Rose have been kidnapped and forced to play terrible and deadly games. But what happens to the bodies of the murdered contestants? And what sinister plot do the games hide? (45 mins.)
 
11.
Doctor Who (2005 TV Series)
Episode: A Christmas Carol (2010)
    1 2 3 4 5 6 7 8 9 10 8.6/10 X  
A space liner, with a large number of passengers aboard, is in difficulties while flying through the atmosphere of an unknown planet... (45 mins.)
 
12.
Doctor Who (2005 TV Series)
Episode: The Waters of Mars (2009)
    1 2 3 4 5 6 7 8 9 10 8.8/10 X  
In a Mars base the inhabitants are being infected by a mysterious water creature which takes over its victims. The Doctor is thrust into the middle of this catastrophe knowing a larger one is waiting around the corner. (45 mins.)
 
13.
Doctor Who (2005 TV Series)
Episode: The Rings of Akhaten (2013)
    1 2 3 4 5 6 7 8 9 10 7.4/10 X  
Still not quite able to explain just who she is, the Doctor and Clara set off on their first adventure... (45 mins.)
 
14.
Doctor Who (2005 TV Series)
    1 2 3 4 5 6 7 8 9 10 7.7/10 X  
The Doctor and Clara find themselves aboard a space freighter that has taken the TARDIS on-board as salvage... (45 mins.)
 
15.
Doctor Who (2005 TV Series)
Episode: The Empty Child (2005)
    1 2 3 4 5 6 7 8 9 10 9.2/10 X  
Rose and the Doctor find themselves in 1941 London when the TARDIS receives an emergency signal from another time-traveling vehicle... (45 mins.)
 
16.
Doctor Who (2005 TV Series)
    1 2 3 4 5 6 7 8 9 10 9.1/10 X  
The Doctor takes Amy and Rory to New York, where the Weeping Angels are waiting for them. River Song returns. (45 mins.)
 
17.
Doctor Who (2005 TV Series)
Episode: The Sound of Drums (2007)
    1 2 3 4 5 6 7 8 9 10 8.8/10 X  
The Doctor, Martha and Jack return to the 21st Century eighteen months after the Doctor and Martha left. They find they've missed the election, and the new Prime Minister, Harold Saxon, is someone they've met before by another name. (45 mins.)
 
18.
Doctor Who (2005 TV Series)
Episode: The Snowmen (2012)
    1 2 3 4 5 6 7 8 9 10 8.5/10 X  
London, 1892. Snow is trying to evolve, feeding off of the nightmares of a little girl. But the Doctor has given up on saving the world. It is up to a young governess named Clara to convince him, with just one word, to save the day. (45 mins.)
 
19.
Doctor Who (2005 TV Series)
Episode: Blink (2007)
    1 2 3 4 5 6 7 8 9 10 9.8/10 X  
Sally Sparrow receives a cryptic message from the Doctor about a mysterious new enemy species that is after the TARDIS. (45 mins.)
 
20.
Doctor Who (2005 TV Series)
Episode: The Unicorn and the Wasp (2008)
    1 2 3 4 5 6 7 8 9 10 7.8/10 X  
With a 1926 dinner party turning into a murder mystery, The Doctor and Donna Noble get the chance to meet Agatha Christie on the eve of her well-known 9-days disappearance. (45 mins.)
 
21.
Doctor Who (2005 TV Series)
Episode: The Sontaran Stratagem (2008)
    1 2 3 4 5 6 7 8 9 10 7.6/10 X  
UNIT's newest recruit Martha Jones enlists The Doctor's help to investigate kid genius Luke Rattigan and his ATMOS system that is used in every car on Earth. (45 mins.)
 
22.
Doctor Who (2005 TV Series)
Episode: Asylum of the Daleks (2012)
    1 2 3 4 5 6 7 8 9 10 8.8/10 X  
The Doctor, along with Amy and Rory who are headed for divorce, are kidnapped by the Daleks. They find... (45 mins.)
 
23.
Doctor Who (2005 TV Series)
Episode: Planet of the Dead (2009)
    1 2 3 4 5 6 7 8 9 10 7.6/10 X  
A meeting in a London bus with jewel thief Lady Christina takes a turn for the worst for the Doctor when the bus takes a detour to a desert-like planet, where the deadly Swarm awaits. (45 mins.)
 
24.
Doctor Who (2005 TV Series)
Episode: The Fires of Pompeii (2008)
    1 2 3 4 5 6 7 8 9 10 8.1/10 X  
Instead in Rome, The Doctor and Donna Noble end up visiting Pompeii in AD 79, on the eve of the catastrophic eruption of Mount Vesuvius, before anyone even knew it was actually a volcano.The entire city is doomed for destruction. (45 mins.)
 
25.
Doctor Who (2005 TV Series)
Episode: The Doctor's Wife (2011)
    1 2 3 4 5 6 7 8 9 10 9.1/10 X  
While traveling in the TARDIS with Rory and Amy, the Doctor hears a knock on the TARDIS doors. Bewildered and no doubt curious... (45 mins.)
 
26.
Doctor Who (2005 TV Series)
Episode: The Unquiet Dead (2005)
    1 2 3 4 5 6 7 8 9 10 7.7/10 X  
The Doctor has great expectations for his latest adventure when he and Rose join forces with Charles Dickens to investigate a mysterious plague of zombies. (45 mins.)
 
27.
Doctor Who (2005 TV Series)
Episode: The God Complex (2011)
    1 2 3 4 5 6 7 8 9 10 8.2/10 X  
The Doctor, Amy and Rory become trapped in a hotel of horrors unable to escape and unable to find the TARDIS. The Doctor must save as many people as he can taking many twists and seeing his own worst fear. (45 mins.)
 
28.
Doctor Who (2005 TV Series)
Episode: 42 (2007)
    1 2 3 4 5 6 7 8 9 10 7.5/10 X  
On a spaceship headed straight for the center of the sun, The Doctor only has 42 minutes to save Martha and the rest of the ship's crew from an inevitable doom... (45 mins.)
 
29.
Doctor Who (2005 TV Series)
Episode: The Shakespeare Code (2007)
    1 2 3 4 5 6 7 8 9 10 7.8/10 X  
The Doctor takes Martha to London in 1599, where William Shakespeare's new play is being used by three witches in an evil plan. (45 mins.)
 
30.
Doctor Who (2005 TV Series)
Episode: Tooth and Claw (2006)
    1 2 3 4 5 6 7 8 9 10 8.0/10 X  
The Doctor and Rose are transported to 19th Century Scotland, where they meet Queen Victoria, and try to protect her from a ravenous werewolf and a band of assassinating warrior-monks (45 mins.)
 
31.
Doctor Who (2005 TV Series)
Episode: Father's Day (2005)
    1 2 3 4 5 6 7 8 9 10 8.4/10 X  
All of her life, Rose's mother told how great a man her father Pete was. He was killed by a hit and... (45 mins.)
 
32.
Doctor Who (2005 TV Series)
Episode: Love & Monsters (2006)
    1 2 3 4 5 6 7 8 9 10 6.3/10 X  
A run in with the Doctor at a young age leads Elton to a group who's studying him, they become friends and have a laugh until Victor Kennedy arrives... (45 mins.)
 
33.
Doctor Who (2005 TV Series)
Episode: Gridlock (2007)
    1 2 3 4 5 6 7 8 9 10 8.1/10 X  
The Doctor takes Martha to New Earth, where she is kidnapped by two carjackers and taken to an underground Motorway, where the remainder of humanity on the planet live in perpetual gridlock. (45 mins.)
 
34.
Doctor Who (2005 TV Series)
Episode: New Earth (2006)
    1 2 3 4 5 6 7 8 9 10 7.6/10 X  
As Rose Tyler embarks upon her first big TARDIS adventure with the newly-regenerated Doctor, they discover a sinister hospital run by strange cat people and run in to two old acquaintances, The Face of Boe and Cassandra. (45 mins.)
 
35.
Doctor Who (2005 TV Series)
Episode: A Town Called Mercy (2012)
    1 2 3 4 5 6 7 8 9 10 7.5/10 X  
The Doctor gets a Stetson (and a gun), and finds himself the reluctant Sheriff of a Western town under siege by a relentless cyborg who goes by the name of The Gunslinger. But who is he and what does he want? (45 mins.)
 
36.
Doctor Who (2005 TV Series)
Episode: The End of the World (2005)
    1 2 3 4 5 6 7 8 9 10 7.7/10 X  
The Doctor takes Rose to the year 5 billion to witness the destruction of the Earth. (45 mins.)
 
37.
Doctor Who (2005 TV Series)
Episode: Rose (2005)
    1 2 3 4 5 6 7 8 9 10 7.6/10 X  
Rose Tyler is just an ordinary shop worker living an ordinary life in 21st century Britain. But that life is turned upside down when a strange man calling himself The Doctor drags her into an alien invasion attempt! (45 mins.)
 
38.
Doctor Who (2005 TV Series)
Episode: School Reunion (2006)
    1 2 3 4 5 6 7 8 9 10 8.4/10 X  
The Krillitanes - aliens with a mix-and-match physiology - are trying to crack the 'God-Maker', a paradigm to give them ultimate power. They are using children as a computer, and only the Doctor and Rose, re-united with Sarah Jane Smith and K9 can prevent them from becoming masters of time and space. (45 mins.)
 
39.
Doctor Who (2005 TV Series)
    1 2 3 4 5 6 7 8 9 10 7.4/10 X  
It's Christmas Eve, 1938, when Madge Arwell comes to the aid of an injured Spaceman Angel as she cycles home... (45 mins.)
 
40.
Doctor Who (2005 TV Series)
Episode: Amy's Choice (2010)
    1 2 3 4 5 6 7 8 9 10 8.3/10 X  
Five years after finally leaving the TARDIS Amy and Rory now married, live in the quiet little village of Leadworth. But everything is not what it would seem. (45 mins.)
 
41.
Doctor Who (2005 TV Series)
Episode: Partners in Crime (2008)
    1 2 3 4 5 6 7 8 9 10 7.8/10 X  
With a new weight-loss pill tested in London by Adipose Industries, The Doctor goes to investigate the sinister truth behind the product, only to find out that his old friend Donna Noble is investigating as well. (45 mins.)
 
42.
Doctor Who (2005 TV Series)
Episode: The Hungry Earth (2010)
    1 2 3 4 5 6 7 8 9 10 7.4/10 X  
The Doctor tries to get everyone to Rio, but nothing quite goes as planned. They arrive in a small Welsh... (45 mins.)