Disable full screen mode and go to your Zen garden and feed the plants. It usually takes 30 minutes after feeding the plants before you are able to feed them again. If you change the system date to an earlier value you will be able to feed ALL the plants and increase their growth.
When you battle the final Boss he will launch large fire balls and ice balls at your plants. These will crush everything in their path except for zombies. To destroy the ice balls use a Chili Pepper in that row. The fire ball is destroyed by using an Ice Shroom but it must have a Coffee Bean or else it will fall asleep.