You missed a good one! I'm not much on details, but Sydney went on a mission that would require calculus to be done in someone's head. I think if she took along any kind of electronic device it would trigger an alarm or something. The only person at SD-6 that was capable of mental calculus was Marshall, so he went along with her. Sydney, knowing that Marshall would report to SD-6 told Vaughn she "wouldn't be able to bring back a fake Marshall," so Vaughn arranged for the FBI to pick up Marshall as he's going home from the airport after they get back to L.A. However, something went wrong and some other bad guys got to Marshall first. The last scene of the show showed the scary dentist guy (the one who pulled Will's teeth last season) face to face with Marshall who is bound to a chair and needless to say very very frightened.
Also, Will took a test to try to work with the government as an investigator.
Anyone else who can fill in some of the details, please do so. I know I left much out!