Following the 2006 season, Wells filed for free agency. For players who are already planning on retiring, this is a customary move in case one changes his mind. Wells' agent had stated the pitcher will keep his options open but his physical condition will play a large part in making the final decision whether or not to return for another season. Eventually, Wells decided to stay with the Padres, agreeing in principle on a one-year deal worth $3 million in base salary with a possible $4 million more in incentives.