YuGiOh Series Question?

Okay i watched the first 2 seasons of yugioh a long time ago, the last episode i watched was wen kaiba was on his blimp and marik and bakura dueled each other. Where has the series gone from here. Because on hulu i was watching the 1st episode of season 5, and joey says "pegasus flew us here" I thought yugi defeated pegasus and then then yugi pulls out the 3 god cards. IM like O_O wtf lol please help...