Add this to your functions.php
file:
add_filter( 'meta_content', 'wptexturize' );
add_filter( 'meta_content', 'convert_smilies' );
add_filter( 'meta_content', 'convert_chars' );
add_filter( 'meta_content', 'wpautop' );
add_filter( 'meta_content', 'shortcode_unautop' );
add_filter( 'meta_content', 'prepend_attachment' );
Then use this code to pull in the result:
<?php $story_content = get_post_meta($post->ID, 'story', true); echo apply_filters('meta_content', $story_content); ?>