I just picked up FFIX again after 3 months. I got up to disc 3, and I'm on Terra, but I've forgotten the whole storyline up to there. Can someone tell me the basics of what happened? And also what do dead peppers do when you feed them to your chocobo? He can climb mountains if that helps.

Just replay the game..

Oh and dead pepper opens cracks, helps the chocobo fly into the sky for Chocobos air gardens, and helps it dive into bubbles.

Okay then... So what do you mean by cracks and bubbles?

http://www.square-enix.com/sei/index.htm

go here. it's the official square site and look at the top there is a pannel of options. one is "online guides" click on it and an options bar will drop down. one of the options is FFIX. after clicking on it it will ask you to sign in/regester, obviously you'll have to regester. and then you'll be able to look at the official online guide, which was written to go alongside the offical guide