If we focus on John Merritt and ask ourselves what kind of person he is, we are asking what he is like inside: his values, beliefs, hopes and fears. The cliche that comes to mind as one of the play's main themes is "Beauty is skin deep." As with all cliches, there is much truth in it, and certainly it pertains to The Elephant Man. What Merritt teaches us throughout the play is that underneath his hideousness, he is someone who cares about the world and wishes to make connections to other people. As he says so poignantly and memorably when chased, "I am not an animal!" Yet he has been treated like an animal his entire life. Even when under the more humane care of the doctor and hospital, he gradually realizes that he is a speciman more than he is a man. His suicide points to another important theme in the play, which is the loneliness of the human condition. We all want to connect with other people, and reading or watching the play, we wince at Merritt's life, so much more painful than anything we endure. We also connect with him because he stands for the terrible loneliness that we are all prey to.
The theme of The Elephant Man is man's inhumanity to man. Any difference in appearance, actions, or intellect appears to some to be carte blanche for treating the person inhumanely. In some cases, this is because a person may have been born without the capacity for empathy. In others, the mistreatment comes from fear, not of the person as an individual, but of the fact that all human beings are susceptible to differences whether by birth, nurture, or accident. Therefore, if a human being is treated inhumanely, he is not human--what has happened to him cannot happen to me, so I am safe as long as I make sure to distance myself from the person and his defect.
Each person who reads this book can find something different in it. One of the themes that stands out is the notion that beauty is only skin deep. Although his physical appearance can be called grotesque, John Merritt has a kind and gentle soul. He is treated horribly by people; yet he is still able to place trust in a few. Ironically, the person he trusts most, Treves, is primarily interested in the attention John can bring to him.
Another theme is loneliness. John yearns for companionship, but he knows that his condition drives people away from him. He spent most of his life in isolation, living alone. His one opportunity at a relationship with a woman is forced to end because of a misunderstanding, and John never tries again to get close to a woman.
The eNotes study guide has a thorough discussion of themes in the book.