That element of the show was on full display in the series six finale "The Wedding of River Song."
The episode began with all manner of time anomalies like pterodactyls, hot air balloon cars, steam trains and Winston Churchill as Caesar. When The Doctor is brought forth as a prisoner, he explains that a women has done something with time. Of course he means River as he begins to tell his story leading up to the events of "The Impossible Astronaut."
This all happens by about five minutes in, and instantly it's the most confusing episode of "Doctor Who" ever. That's saying something on a show about an immortal time traveler whose blue police box spaceship is bigger on the inside.
Once it is revealed that it's indeed River in the astronaut suit, she decides not to kill The Doctor and everything goes "wibbly wobbly timey wimey" and it's back to Churchill Caesar.
With all these crazy time problems the Silence aren't far behind and naturally mysterious marks begin to show up on The Doctor's arm. Fortunately, Amy and Rory show up as kickass commandos and save the day.
In the new timeline Amy remembers The Doctor and Rory but doesn't recognize the awesome Capt. Williams as her parents.
Let's take a moment and discuss the complete badass that Rory has become. When he stayed behind to fight off the escaping Silence he officially won the title of best companion ever. Arthur Darvill is so spectacular at simultaneously portraying Rory the heroic "last centurion" while also never losing site of the dorkiness that makes him so lovable.
In the end The Doctor had to convince River to let him die so that time could be reset. Before she agreed to do it, he married her and shared his plan to have a Tesselecta robot take his place.
He later explained that he had gotten too big and famous and it was time for his to go back into the shadows. This comment signaled a return to The Doctor's roots as a secret operator who doesn't like extra attention.
The best of the rest:
- The Doctor wasn't ready to say goodbye and said he could help Rose Tyler with her homework or go to all Jack's stag parties. I bet Jack has the best stags.
- It wasn't until he heard about the death of the Brigadier that The Doctor accepted his fate. This was a nice tribute to the late Nicholas Courtney.
- Amy's line before she killed evil eye patch lady was so satisfying. "River didn't get it all from you sweetie."
- It's nice to see that River visits Amy and Rory and calls them mom and dad.
- Steven Moffat cleverly hid the answer to everything in plain sight in regards to The Doctor's death.