Iron Man faces Madden Mallen for the second time but this time and thanks to Extremis and his new armor conducted by thought, it is Mallen who's soundly defeated. At the end, Tony Stark has no option but to kill Mallen by destroying his head.
Finally, Iron Man gets Maya Hansen arrested for being the accomplice of Dr. Killian. Without further funding from the Army, they decided to field test Extremis against the most advanced personal combat system in the world: Iron Man. And sold the that super soldier serum to a terrorist. Maya tells Tony that she would have used the extra funding to stop manufacturing weapons and devote her research to medicine, so he's no better than her. But Tony replies that he is trying to be, and his conscience is clean.