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Fiona's father King Harold doens't necessarily want to kill Shrek; Fairy Godmother does. She helped him with his "happily ever after," by tranforming him into a human so he could marry Queen Lillian. The Godmother wanted Fiona to marry Prince Chraming, her son, so she wanted Harold to "get rid of" Shrek. If he didn't go along with her plan, she would take away his happily ever after, and transform him into a frog, his original form.