A Great Tragedy
Summary: Spock suddenly understands how everything was a great tragedy. (Spock POV).
Disclaimer: Nope, I don't own Star Trek: Into Darkness or any of these characters. Cause Spock beating Khan scared me so much!
Spock knows that Captain Kirk can be illogical, driven to questionable acts that he can conduct. He's still not sure how dealing with Khan will lead to the greatest tragedy for them, but he'll be on the watch. He'll make sure that Kirk will not be manipulated by Khan.
He knows what he has to do.
Vulcans do not lie, but he's not technically lying when he tells Khan that he can have his 72 torpedoes. He may have misplaced Khan's crew members, but he won't let Khan destroy his crew members or Captain Kirk, so what if he misdirected Khan into thinking he has his own crew members back. A little bit of misdirection cannot hurt. He also knows that intellect aside will not help him defeat Khan.
But when he sees Kirk lying on the compartment, dying from radiation poisoning, is when a tear drops, he understands perfectly.
He understands how this day is the greatest tragedy of all. And he'll get back at Khan for this.