At the end of the story, Charlie returns by mistake to his old class with Miss Kinnian. He is again mentally handicapped and temporarily forgets that he had an operation that made him much more intelligent. He forgets that he left the night school.

When Miss Kinnian sees him sitting back in her classroom as if nothing has happened, she runs from the room crying. It breaks her heart to see Charlie in his old state after he had come so very far intellectually. In addition, when he was highly intelligent, Charlie and Miss Kinnian had dated and started to fall in love. Charlie doesn't remember this, but Miss Kinnian must be heartsick to think a man she might have built a life with is now once again in a childlike and dependent state.

Charlie describes the scene as follows in his journal:

She startid to cry and run out of the room and everybody looked at me and I saw they wasnt the same pepul who used to be in my class.

Then all of a suddin I remembered some things about the operashun and me getting smart and I said holy smoke I reely pulled a Charlie Gordon that time. I went away before she come back to the room.

In the story, Flowers for Algernon, Charlie is the main character and Miss Kinnian is his teacher.  At first, Charlie does not understand much of school but tries hard.  Miss Kinnian recommends him for a scientific experiment to raise his intelligence.  That is successful for a while, but then fails and Charlie returns to what he was.

When Charlie shows up at school, Miss Kinnian is taken aback as Charlie sits in his old seat and picks up his old books.  She knows how intelligent Charlie was as a result of the experiment, and it hurts to look at him trying so hard again with so little intelligence or aptitude for school.  Seeing her aghast reaction, Charlie remembers that he no longer goes to this school.  She tries to soften the blow for him because he was her favorite student, but he leaves anyway.  She is left to wonder what happens to him as he does not return.  I think she wonders whether she should have disturbed Charlie in his innocent first life before the experiment when he was happy on his terms.