Let's see if I can remember. They found the plane and only half of the missiles (50 out of 100). Mac asked if the others were possibly destroyed in the crash, but they said no as the others were fully intact. So we have to assume that they were stolen by someone.
The guy who was giving Mac's buddy a hard time was a pal of Templeton's and needed his and other Republican's support in order to win his next election. His opponent apparantly has a lot of money and would be difficult to beat. So Mac offered his opponent the Secretary of Treasury position bascially ensuring that the Templeton's buddy would win. So then Mac told him to lay off her guy.