There are a total of 7 main stories in the Ultimate Story, along with at least 1 side-story in between. The main stories are as follows:

Ultimate Story: The Beginnings-The story starts out as Lisa Simpson and her friends setting out on a journey to stop a terrible evil from threatening the Earth

Ultimate Story 2: The Revelations-This story starts out with the journey on Dinosaur Planet and ends with the defeat of another terrible evil that threatens the entire Universe, starts out with Starfox Adventures

Ultimate Story 3: Aid from the Past-An unusual turn of events that causes many time lapses eventually affected the balance of the        Universe that caused some places to age rapidly and others to remain frozen in time

Ultimate Story 4: Kingdom Come-Mysterious Dark creatures have been reeking havoc in many worlds, causing them to undergo a               deterioration process that must be stopped, involves setting from Kingdom Hearts

Ultimate Story 5: The War Against Darkness-A war within another dimension caught the attention of many who have allied themselves with the Light and must stop it before other worlds become affected by it, a side story is involved in this

Ultimate Story 6: The Great Collapse-All worlds inexplicably collapsed and all those who have allied themselves with the Light are left to find out what caused it while resembling everything, the first appearance of Super Mario Galaxy's own Rosalina

Ultimate Story 7: The Ultimate Battle-All heroes and allies become part of an epic battle to ultimately decide the fate of the Universe, the final chapter of the Ultimate Story