When the original Great Fox was destroyed by ramming a shield in the Aparoid homeworld, allowing the members of Star Fox to enter and kill the Aparoid Queen, a second mode of interplanetary transportation was needed. The Great Fox II was used for being much cheaper then the costly Great Fox, and was practically a decommissioned warship used by the Cornerian army. All of it's armor and weapons had been stripped, and the ship was forced to use inexpensive long range bombs instead of actual lasers. The Great Fox II assisted with taking on the barren planet Venom in order to overthrow the Angler queen during the Angler Blitz.
After the events of Star Fox: Command, the Great Fox II was sucked into a Portal, and had to crash land on Gauss Wisely. It was completely destroyed, and only a few spare Arwings, weapons and the processing unit that madeup ROB 64's personality survived. Whatever was left was sold for scrap, so Fox could buy a new and much smaller corvette that could hold the few ships, weapons and scrap that he still had.
The Great Covenant-Human Autumn-Class Tactical Asteroid eventually replaced the ship, after Fox joined Team Heretic Dinofox. It's legacy was carried on to the Great Fox III, which resembled the original Great Fox rather then the second one.