Now that you've decided that it's in the best interest of your story to hurt your bunny, your main character, how do you do it?
This is the most obvious way. You can make your character sick with the flu or pneumonia. You can break his leg or sprain his ankle. You can give him a rash, a bee sting, or allergies.
This one can be divided into two closely related illnesses: mental and emotional. I'm not a psychologist, but I've watched one on TV. So, you'll probably have to do some research on these to be sure you're calling the illness the correct name.
Your bunny could have a mental illness, such as multiple personalities (and since bunnies multiply rapidly, your bunny might have a dozen or so before your story is over) or an eating disorder (too many carrots). Perhaps it's depression or OCD or post traumatic stress disorder.
You might have your bunny suffer from a bully who steals his lunch money or has low self-esteem. Perhaps your bunny can't tell the truth and just has to exaggerate everything he says. Your bunny might be a hypochondriac. Maybe he fears small spaces or is afraid of tornadoes.
That's right; you can even hurt your bunny spiritually. Things can get so bad for him that he may doubt God...or the conflicts might turn him toward God or toward something else.
Now, when you hurt your bunny, don't do it randomly. Plan on ways to hurt your bunny that will also advance your plot. Before you write, it's a good idea to do a character sketch of your main bunny. Figure out what your bunny's strengths and weaknesses are, what his dreams and fears are. Now you hit him where it hurts: confront him with his weaknesses and his fears, make his dreams appear to evaporate, turn his strengths against him.
Your reader will love you for it!