Andross is back and full of malicious intent on getting revenge at the Star Fox team, as is the evil General Scales. The duo has united and have set a trap for the Star Fox team. Since the destruction of Krystal's home planet and the mysterious murder of her parents, she has joined forces with Fox McCloud, Falco Lombardi, and the rest of the Star Fox team. (You'll see this in Star Fox: Adventure and Star Fox: Assault.) Andross has used his powers to create a new planet, Cerinia 2. After the destruction of Krystal's home planet in Star Fox: Adventure, she becomes curious about this newly created planet. (Her home planet was named Cerinia.)
Falco agrees to accompany Krystal as they make their journey to Cerinia 2. There, they are attacked by General Scale's goons, members of the SharpClaw tribe. Falco is knocked unconscious, while Krystal is left to defend him and herself with her staff. Upon defeating the group of SharpClaw dinosaurs, she discovers another lying in a small patch flowers, similar to the scene in Star Fox: Adventure where Fox discovers Krystal's staff. She picks up the staff, with difficulty. A bright, large beam of light eminates from the staff, and fills the entire screen. It can be guessed that the staff teleported Krystal and Falco back to the Star Fox ship, as that is where the next scene takes place.
The newly acquired staff of Krystal's was created by Andross himself. He and General Scales designed the setup with the idea that naming the new planet, Cerinia 2, after Krystal's now-destroyed home planet. The idea was to draw the Star Fox team, Krystal particularly, to Cerinia 2 so that Andross would be able to then destroy Star Fox. Obviously it did not go as planned, as Krystal and Falco survived and narrowly escaped due to the magical staff Krystal now possessed.
The mystical staff has properties similar to Horcrux from the Harry Potter universe. When Krystal brings it back to the Star Fox ship, it takes the effect of putting the Star Fox team in a bad mood, with the exception of ROB (the staff doesn't effect robots.) Like Ron Weasley, who leaves Harry and Hermione Granger because of the effects of the Horcrux, the entire Star Fox team splits up because of the effects of Krystal's staff.
Now Fox and Krystal must set out and find the rest of the Star Fox team and reunite them in order to defeat Andross and the staff.