A few years after the events of Star Fox Assault, Fox and Krystal got closer. Apparently, at some point, Fox realized that he liked Krystal far more than he was prepared for and grew afraid that Krystal might get hurt in the mercenary line of work. Not thinking things through, Fox pushed Krystal away, forcing her to leave the team despite her protests.

This action, along with the slowdown of work after the war, caused the Star Fox team to break up. Falco once again went off on his own. Slippy moved to Aquas, where he met a lovely toad named Amanda and began to settle down. Fox and Rob wandered Lylat in a new ship simply called the Great Fox, which beared no resemblance to the original.

During this time, unbeknownst to anyone, Krystal quietly either joined the Cornerian Air Force and received a fighter much like Bill Grey’s, or simply stole one. When Krystal did resurface, she had joined Star Wolf. While she may have had many different motives for joining them, the only one we are certain of is that it would hurt Fox emotionally when he found out. Something happened between Krystal and Panther, but it’s unknown what. Panther, during this time, began acting rather strange, referring to himself in the third person.

Shortly after or during all that, a new threat from Venom’s oceans was discovered. The Anglars attacked. You begin the game as Fox and Rob struggling to do something about this new threat. Depending on the paths you choose, Krystal can have one of several fates (as does everyone else).

In some paths, Fox begs Krystal to return. In others, he is stubborn to the point of not caring. She may or may not rejoin depending on the choices you make. Krystal grew cold-hearted during her time with Star Wolf. Originally, she only joined them to hurt Fox, but she, in some missions, seems to genuinely care about their wellbeing. In one ending, Krystal and several other women in the series defeat the Anglars themselves. Afterward, Krystal and Fox make up. In another, she leads Star Wolf to victory after discovering one of Andross’s devices, but is later viewed as a traitor to Star Fox. She can’t stand the criticism and goes to another galaxy to become a bounty hunter named Kursed. In still another ending, Fox disbands Star Fox again to pursue Krystal on Sauria where they marry and have a son named Marcus. In the default ending, which you are forced to do first, Krystal rejoins Star Fox only to leave for Star Wolf again at the very last minute. Finally, one ending results in Krystal rejoining the Star Fox team after accepting Fox’s apology, and the team goes back to the way it was during Assault.

No-one knows which, if any, of these storylines will be the offical canon one. We probably won’t know for sure until at least the next Star Fox game. It’s also very hard to explain the various scenarios, because there are 18 possible ways to get to the nine different endings. If you haven’t already played the game, the best way to understand the story is to visit the Star Fox Command: All The Words page, which has the complete script for the game.