I got this out of PeTeRL90's walkthrough. :P

How to get KratosTo get Kratos, you should've have broughten him with you way back when you fought Kvar. If you did, then you'll recive some knocks on your doors. The first will be Colette. Decline her. The second will be Genis. Decline him. The third will be Sheena. Decline her. Now Lloyd will stare out his window, and he'll hear a voice. Kratos's voice. He'll head outside, and then a long scene between Lloyd and Kratos starts. It's mainly about how Kratos meet Lloyd's mom and whatnot. Also, if you want, you can view each of the other characters scenes, but make sure to reset the game after each one until you get Kratos.

Basically, this happens in Flanoir, so you'll have to deal with Zelos for a good portion of the game