Dr. Who - What's been going on

The second part of Matt Smith's second season premiers tomorrow. This is a good chance to point out some of the background plot threads.

There are two major threads that have spanned multiple seasons. The first was River Song. When we first met her we learned that she would marry a future version of the Doctor. In her next appearance we found out that she was in prison for killing "a very good man." This was never explained but the implication was that she would kill the Doctor himself.

The second thread is the Doctor as a dangerous being. There were a few hints of this earlier but Smith's Doctor spent a lot of time saying it. In his first episode he saved the Earth with just a borrowed cell phone. Afterwords he warned some powerful aliens that they should avoid the Earth because he protected it along with the implication that he was someone to be feared.

Later he told a group that the Weeping Angels made a mistake by trapping the one person in the universe that they should not want trapped. Statements like this were peppered through the season. There have also been reminders that he killed his entire race.

In the season's two-part finale, the Doctor traveled to Roman Briton to see the Pandorica, the ultimate prison, opened. He didn't know who was inside but he wanted to protect the universe against that person. Multiple races encircled the Earth for unknown reasons.

Surprise - the Pandorica was meant for him. All of these races considered him the most dangerous being in the universe. Things got confused when an unknown entity also tried to destroy the universe by exploding the TARDIS. The Doctor rebooted the universe and reappeared in time for Amy's wedding party.

In the season opener we saw a much-older Doctor gather a few friends including Amy, Rory, and River. He and River compared diaries and he had already experienced all of their shared time. Then he was killed by a figure in a spacesuit. And killed a second time to prevent regeneration.

But this was a future Doctor. His younger version was still running around. Amy and River put him on the trail of the figure in the spacesuit. This turned out to be an unusual girl who could regenerate. The girl looked a bit like a young River but her effects and the attention of some aliens hinted that this would be Amy's daughter.

At one point Amy told the Doctor that she was pregnant which she later denied. The Doctor took some readings which he kept secret but kept referring to.

Eventually we found out that the Amy on the TARDIS was a reproduction linked with the real one. The real Amy was pregnant and being kept prisoner somewhere.

It all came together in the Demon's Run episode when we found out that Amy's daughter Melody Pool was also River Song.

So, here's what happened. Some aliens took the Doctor seriously when he said that he is the most dangerous being in the universe and decided that they needed a weapon to kill him. Only a fellow Time Lord could do this but he already killed all of them so they had to create a new one. Because she was conceived in the TARDIS while it was traveling through time, River shared many of the mutations that make up a Time Lord. So the aliens kidnapped Amy between seasons and left a decoy to keep the Doctor from suspecting. They raised the child and eventually she fulfilled her destiny and killed the Doctor.

But, since River was a partial Time Lord, things were not that simple. She and the Doctor met at multiple points of their lives, often in opposite directions. The first time he met her was just before she died. The first time he kissed her was the last time she kissed him, etc.

It is unclear if Amy will ever see River again as a child. It looks doubtful since River didn't recognize Amy or Rory as her parents when they first met. She had to be introduced.

BTW, the space station is misnamed. It isn't "Demon's Run". It should be "Demons run" from the 'old' saying "Demons run when a good man goes to war."