In Battlestar Galatica Pegasus expansion, does the cylon team win if the cylon leader wins?
The Cylons and the Cylon leader win the game, together. The Agenda Card condition indicates which side they favor. They will have another condition which seems counter to their allegiance, but they are predominantly on one side or the other. 

From page 10 of the Pegasus rule book:


  Note that Cylon Leaders may win with the humans or the Cylons, as
  specified by their Agenda Card.