You'll want to use JavaScript's Array splice method:

var tag_story = [1,3,56,6,8,90],

    id_tag = 90,

    position = tag_story.indexOf(id_tag);



if ( ~position ) tag_story.splice(position, 1);

P.S. For an explanation of that cool ~ tilde shortcut, see this post:

Using a ~ tilde with indexOf to check for the existence of an item in an array.

Note: IE < 9 does not support .indexOf() on arrays. If you want to make sure your code works in IE, you should use jQuery's $.inArray():

var tag_story = [1,3,56,6,8,90],

    id_tag = 90,

    position = $.inArray(id_tag, tag_story);



if ( ~position ) tag_story.splice(position, 1);

If you want to support IE < 9 but don't already have jQuery on the page, there's no need to use it just for $.inArray. You can use this polyfill instead.