first off, the javascript_include_tag for prototype is redundant, as prototype is included in the defaults.
second, try this
<div id="my_div">This will go away</div> <%= link_to_remote "Do Magic", :url => {:action => "DoMagic"}) -%>
then in your controller:
def DoMagic render :update do |page| page.visual_effect :fade, 'my_div', :duration => 1.5 end end
your browser will make an ajax request when the link is clicked, the server will respond with some javascript which will be evaulated and your div should fade out.