At the beginning of the story Charlie was mentally handicapped and diagnosed with an IQ of 68. He was 32.
For a man with mental retardation (as explained in the story), he was incredibly motivated, making sure he worked hard at a Special university and making tasks to be selected for a surgery which would triple his IQ.
After the surgery, the first sign you see is that he is operating complex machines, and his IQ begins to increase. Most importantly, he beat Algernon in completing a maze: Algernon is a rat who underwent the same operation as a test variable.
Yet when you put into perspective that Charlie went from two completely different sides of life (from mentally challenged to genius) in just months, you can imagine the changes that impacted his personality.
First of all, he would see people for who they really were. He understood now all the digs that were thrown at him in the beginning, and the double entendre of many jokes. He changed, because he wanted desperately to be taken seriously. In a way, he shun everyone who was one his friend so that he could eradicate that part of his life.
Equally, he fell in love. When he did, he overanalyzed and over complicated things because his mind would work so fast and with such complexity that he was now losing friends, and his attitude continued to change.
When he realized the mistake in the hypothesis that would contribute to his increase in IQ, his anger was not just directed at the doctors, but at himself, at the society who laughed at him once, and at all of those whom he once loved.
As his condition deteriorated again, he came back to being a simple man, almost childish, still in pain for what was gone, but most importantly, he was returned to a state of innocence that begged for the mercy of Algernon, rather than for his own.