This is the next chapter to the Ultimate Story. This chapter starts out with the events of Starfox Adventures. In this story, Fox McCloud, joined by Misty, Bubbles, Princess Peach, Rayman, Banjo, Kazooie and Pikachu, set off on an adventure on a newly discovered planet known as Dinosaur Planet to save the planet from the tyranny of General Scales. Along the way, they meet new friends and allies, Krystal and Tricky. Krystal reveals that she is Fox's sister who was forced to evacuate Corneria after Andross attacked the planet. She becomes a new member of the Starfox team and a very invaluable ally as she has special abilities of her own. Everyone else's powers continue to grow as they learn of other advancements to their powers and continue to use them to fight evil.
As the story continues, the Starfox team learn more about their enemies, the dark wielders, such as their deep influence with the humans as well as the entire planet that they live on. They make even more friends and allies along the way. They have continued their relationship with the girls of GROUP, Sam, Alex and Clover and continue to work with them.
New stories that join the story are Scooby Doo, HiHi Puffy AmiYumi, YinYanYo, The Replacements, Chaotic, Total Drama, WITCH, FFX, Spider Riders and Sly Cooper. (The list does NOT end there; this isn't even half of what shows become part of the story. This is why I find the Ultimate Story to be a fitting name, as generic as it sounds)
They find out about a terrible incident known as the Rifter, which all magical beings have known as the End of All Existence. Eons ago, a terrible evil being known as the Shaman Emperor wanted to destroy all of existence but was thrown into the Shadow Realm. He was released from the Shadow Realm and attempted to eradicate everything. A lot of worlds were destroyed from this while a lot of the surviving worlds were fused together as a means to put a stop to the Rifter. The Shaman Emperor was forced back into the Shadow Realm, but he was to be released again.
They also learn of a group of Dark Wielders known as the Descendants of Darkness, who have played a major role in causing the Rifter. One such member they came across was Neela, a terrible woman who Sly and his friends have defeated in the past. Overtime, they learn that a terrible enemy that they have been dealing with was a member of the Descendants of Darkness and has made strides to release the Shaman Emperor from the Shadow Realm again.
The story ends with Fox, Misty, Krystal and Falco defeating the Shaman Emperor and putting an end to the threat of the Rifter once and for all. However, the story was still not over as there were many more enemies to be faced.