In your secondary the remaining yeast in the beer continues to convert the remaining sugars, usually more complex sugars, to alcohol. They also will continue converting other by products of primary fermentation into complex molecules which provide beer with distinctive styles. Lagers are the most common example of this. During your secondary fermentation the majority of yeast will coagulate and drop of of suspension as well leaving you with a much more clear beer. For ales, this clarifying process is often the only reason for doing a secondary fermentation. After your secondary fermentation you could do a 3rd fermentation to clarify more, but almost no brewers I know use tertiary fermentation except in specialty cases, yet virtually 100$ do secondary ferementations.
After your secondary fermentation it is either time to bottle, or what is a much more effective and easy option keg it
Last Updated: July 12th, 2006