The Aparoids' takeover and apparent eradication of Sauria and its defences in Star Fox Assault. We know the dinosaurs fought back, we know they lost. However, it is more than just a simple case of inverting Rock Beats Laser. The objective of the mission for Star Fox (or rather Fox and Krystal on the ground) is to destroy the Aparoid Hatchers, which enable them to multiply and spawn more troops. Peppy even directly states that "if we can destroy those Hatchers, we might just have a chance". The mission finishes the moment all the Hatchers on Sauria's surface are destroyed. Star Fox had experience combatting the Aparoids prior, they knew what to look for in order to gain an advantage or victory over their enemies. The dinosaur tribes of Sauria, on the other hand, had no such experience, and were facing an enemy that was technologically superior to them, and was capable of replenishing their troop numbers almost instantly, as opposed to their own numbers. The invasion was already well underway long before the Star Fox team got there. It wasn't a straight-up Curb-Stomp Battle, the Aparoids won through sheer numbers and inexperience on the part of the planet's protectors.
This mainly applies to whether one subscribes to the idea that James McCloud was Killed Off for Real prior to the beginning of Star Fox 64. In the definitive climax of the game, Fox is led to safety from Andross's exploding base by what appears to be the "ghost" of James in his Arwing, which disappears as soon as Fox is safe. Now, if James truly was a ghost here, why would he show up on Venom? If the prologue is accurate, then it's because that is where he died. And his last act before passing on to the afterlife is ensuring his son survives and giving him some touching parting words.