Checkmate
Commodore
The TARDIS' Soul: There's been multiple hints and suggestions that the TARDIS had a mind of its own, both in the revival of the series and the older ones. The only thing 'silly' was the ease in which House was able to separate it from the machine itself. If all it takes is an empty vessel, there shouldn't be any trouble repeating it through Time Lord technology. But I'm okay with that.
Not Knowing About the Dead Time Lords: Do you know when every human being goes missing or dies? You sure don't. Now imagine if many of those same human beings can be at any point in the universe (or other universes), at any point in time. Would you know when they were dead? Or even missing? Every. Single. One?
Locking Amy & Rory: He did that because he knew this place was dangerous -- dangerous enough that several Time Lords met their fate here. Considering that he firmly believed the TARDIS to be the safest place in all existence, why not lock them away until he could figure out what was going on? It was a sign of how much he cared about them.
Running: House told them to run. And they did, because they were afraid of what he would do to them if they didn't, which was only driven home later when he displayed the ease in which he could kill them.
Caring About Life: Congratulations, you've picked up on a new aspect of the Doctor's personality that's slowly been building up for a while now. He's no longer afraid to kill if he needs to, especially in retribution for harming him or those he cares for (including the entire Human race). Where exactly this personality trait came from, I don't know. But I've noticed it since at least the end days of the 10th Doctor when he was going all "I'M A GOD!" crazy.
Not Knowing About the Dead Time Lords: Do you know when every human being goes missing or dies? You sure don't. Now imagine if many of those same human beings can be at any point in the universe (or other universes), at any point in time. Would you know when they were dead? Or even missing? Every. Single. One?
Locking Amy & Rory: He did that because he knew this place was dangerous -- dangerous enough that several Time Lords met their fate here. Considering that he firmly believed the TARDIS to be the safest place in all existence, why not lock them away until he could figure out what was going on? It was a sign of how much he cared about them.
Running: House told them to run. And they did, because they were afraid of what he would do to them if they didn't, which was only driven home later when he displayed the ease in which he could kill them.
Caring About Life: Congratulations, you've picked up on a new aspect of the Doctor's personality that's slowly been building up for a while now. He's no longer afraid to kill if he needs to, especially in retribution for harming him or those he cares for (including the entire Human race). Where exactly this personality trait came from, I don't know. But I've noticed it since at least the end days of the 10th Doctor when he was going all "I'M A GOD!" crazy.