What, most likely, was Holden suffering from throughout the novel and how did this affliction tie into the central conflict?
In The Catcher in the Rye, Holden Caulfield struggles to deal with several things which include the death of his younger brother, the suicide of a classmate and the natural consequences of his own actions.
When Holden flunks out of Pency High, he cannot face his parents. This inability to accept the consequences of his actions leads him to his wild three days in New York City.
During this time, Holden reflects repeatedly on the life and death of his younger brother, Allie. At times of peak stress, Holden talks to the dead Allie and calls on him for salvation when he fears that he is disappearing. These repeated episodes demonstrate Holden's unwillingness to accept the fact of his brother's death.
His preference for reality to be something other than it is can be said to drive every conflict Holden encounters and to constitute the deeper conflict of the novel (and of Holden's character).
The myriad negative opinions that Holden expresses in the novel serve to substatiate the notion that he cannot accept reality as it is. He would prefer that his brother were still alive. He would prefer that people would not act phony. He would prefer that people don't tell him "Good luck" instead of saying "good bye". The list of Holden's preferences is a long one. Despite the potency of his convictions, Holden cannot change his reality. He is capable only of sinking more deeply into depression as the list grows.
We might describe Holden's anxiety as a state of depression brought about by a set of negative events (Allie's death, the classmate's suicide, and his expulsion from Pency). This depression leads Holden to avoid the necessary homecoming to his parents home and to reject many of the values that characterize his reality.
Another way to state Holden's problem is to say that he is incapable of identifying with the world he lives in.
In the repressed post-World War II American society, Holden's hatred of phonies and unwillingness to tolerate them sets him apart.
Holden objectifies nearly everyone he meets or thinks about, sympathizing only with children and with the dead.