Maleficent isn't even proclaimed a villain in BBS. They probably meet her at Enchanted Dominion: While going through the castle they meet the evil witch. Who(Maleficent)finds Terra in Aurora's room, they talk. Terra has a pit in his stomach and he thinks the old bat is hiding something, so plays along with it until he finds the reason why(why he looks evil). So later Maleficent gives the trio a hint on finding the cure for Aurora's awakening(maybe MX is hunting her, so the trio is trying to bring her to safety). Aqua and Ven thinks she isn't evil and go to wherever Terra tries to stop them but they bring him along. And they go some-where that has a boss/enemy, or a place with a bunch unbirths. Or just a trap... Only Aqua escapes and looks for Maleficent(dragon).
More assumption/fanfic than theory, though.