One of Star Fox Adventures' most infamous scenes is within the final Krazoa Shrine at Krazoa Palace where Fox McCloud is about to engage in combat with General Scales, seemingly the game's antagonist and final boss, only to be suddenly interrupted by Andross' spirit, who forces Scales to give the last Krazoa spirit to Fox, abruptly ending the fight. Per admitted by developers of Star Fox Adventures during a February 2008 edition of Rare's Scribes, Scales was meant to have a proper boss confrontation, but this was scrapped entirely due to the impending Microsoft buyout that was announced in September 2002, forcing the team to focus on only the Andross boss fight.

However, looking further into Dinosaur Planet and Star Fox Adventures' development cycle, one can see a more complex story going on in regards to the notion of General Scales having a boss fight. The Dinosaur Planet condensed story promises a true final confrontation between Krystal and General Scales within the Desert Force Point Temple, as she places her final SpellStone. After Scales' defeat, the King EarthWalker would barge in and tell Krystal to take his belt (that was provided by Drakor), but then it would turn into stone, resulting in the player into having to swap over to Sabre's story, who takes it to the mutant Shabunga in Willow Grove to help reactivate it, which allows him to enter Dragon Rock unharmed.

However, the leaked December 2000 build of Dinosaur Planet features no such boss fight for Krystal's final visit to the Desert Force Point, instead having a cutscene where Krystal, Scales and Kyte are teleported outside of the temple after the former places the final SpellStone. Krystal plummets into a nearby pond safely, but Scales falls onto a rock and breaks his back, completely incapacitating him. Instead of the King EarthWalker, it's the BoneHead SpellStone guardian who first appeared in CloudRunner Fortress that instructs Krystal to take the Kamerian belt to Sabre so he can have Shabunga revitalize it, as Scales whispers that he'll have his revenge as he passes out.

When Dinosaur Planet was being transitioned into Star Fox Adventures over on GameCube, unused voice clips and also hints found within the 2002 E3 kiosk indicate that Rare planned on revisiting Scales having a boss fight by essentially doing a rematch against his flying galleon like in the game's prologue, though instead of playing as Krystal flying on the CloudRunner, it'd likely would have been Fox in his Arwing. The voice lines reveal that Falco Lombardi would actually appear earlier than in the final game and assist Fox in taking out Scales and his galleon. After Scales' defeat, Fox would land in Krazoa Palace and partake in the Test of Sacrifice, which is where the General Scales "boss fight" occurs in the final game.

Curiously, the 2002 E3 kiosk shows that the dev team had later hoped to include a 1-on-1 fight on-foot against Scales. The fight is very incomplete and Scales is strangely smaller in size than usual, but he will actually attack the player in this version instead of simply walking towards Fox and assuming a fighting stance. He has a number of unique attack animations which aren't used in the final game, though these attacks don't connect with the player. He can be attacked without immediately activating his defeat cutscene here, and will block most of the player's attacks and recoil when an attack is successfully landed on him. His health doesn't seem to decrease, so there doesn't appear to be a way to end the fight.