Representation and Themes
The Doctor Who logo appears in a metallic silver colour, to represent
the Gunslinger, who is a Cyborg. Just after the episode title appears,
the TARDIS materializes into a deep red coloured vortex. This could
possibly be foreshadowing the theme of war, sin and the increasing
amount of rage emitted by the Doctor.
The episode delves into some of the major themes of Doctor Who.
The most important, of course, being the Doctor’s relationship with his
companions and how they bring out the best in him, highlighted by Amy
when she, surprised by the Doctor’s decision to give up Kahler-Jex says,
“This is what happens when you travel alone for too long.” What was
particularly powerful about how it was explored here is that Amy, the
Girl Who Waited and who generally takes the tack of punishing those who
wrong her was the one who reminded the Doctor of his better self.

Meanwhile, Rory, the one who is generally considered more noble was
ready to turn Kahler Jex over without a second thought. The writer did a
great job of showing that moral questions like this are not black and
white; that even in the case of war criminals, people are multi-faceted
and not all good or evil. This was summed up as Isaac lay dying
after being shot by Kahler Tek. He says to the Doctor, “You’re both good
men. You just forget it sometimes.” The Doctor and Kahler Jex are more
alike than he would like to admit, as they both make difficult,
sometimes morally dubious calls for what they consider the greater good.

There’s one line of the Doctor’s that highlights the second major theme
of the episode. When Kahler Jex tries to explain himself and why he
wanted to stay in Mercy to help the people there, the Doctor yells, “You
don’t get to decide when and how your debt is paid!” This is true, and
it’s interesting coming from the Doctor, because he spends a lot of time
trying to compensate for the times when he’s made morally dubious
choices by trying to Save the Universe. The entire reason why the Doctor
felt the need to turn Kahler Jex over to Kahler Tek in the first place
is because he himself was trying to repay a debt to all those that died
because of him.
(I'm running out of relevant gifs/pictures. But i though this was cute!)
The other thing that stood out to me with regard to the Doctor’s
character is that he genuinely didn’t know what he was capable of in his
Moment of Truth. When he forces Kahler Jex out of town at gunpoint, and
Jex says asks if he would really shoot him, the Doctor says “I
genuinely don’t know.” The Doctor uncertain is always an interesting
thing, especially when it’s about himself, since he spends most of the
time acting like the Cleverest Being In the Universe.