Well, we knew it was coming so this was hardly a surprise the game literally set this moment up from the very second level. I definitely appreciate that Karajan is not shown as a combatant at all. Every time you get close he retreats unless finally he is trapped in a box of his own devising. This was never going to end well for him because he was up against a video game protagonist. Someone who can never lose since they just reload whenever mistakes are made.
Now with that done I am sure that Mark will head back to Ninjatown, commit seppuku and everyone (else) will live happily ever after. It is not like the game has been hinting that your Master has been up to something or anything.