Consider the past actions of the Comedian in the film. He is totally loyal to the government. Look at the fact that he assassinated Kennedy because Kennedy was thinking of closing down (or making less influential) the FBI. And so many other things he may have done under the guise of "For the good of the government". From his comments he is also very anticommunist.
Now he discovers a plot that not only goes against the government and his country, involves Russia, and forces both America and Russia to make peace and co-operate. All set up by people who he felt he could trust.
It would go against everything he believes in. There is no one who he can talk to (except past criminals like Moloch) which again aggravates his sense of betrayal.
Essentially - for a man who has charted his own destiny - he finds that he no-longer has control of his future. All that he has believed in is going to change and there is a high probability that he will not be a part of it.
So he starts to crack, and the others are faced that they will have to take him out.
If one considers Rorschach - The Comedian is almost his double except that the Comedian is on the side of 'Good' and Rorschach is on the side of 'Bad'.